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Tang Y, Yu G, Zhang X, Wang Q, Tian D, Tian J, Niu S, Ge J. Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:653-662. [PMID: 30092521 DOI: 10.1016/j.scitotenv.2018.07.437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/30/2018] [Accepted: 07/30/2018] [Indexed: 05/02/2023]
Abstract
Because of increases in atmospheric nitrogen (N) deposition worldwide, nutrient imbalances and phosphorus (P) limitations in soil are aggravated, with the result that P fertilizer applications to terrestrial ecosystems worldwide may increase. Nitrification and denitrification in soil are major sources of nitrous oxide emissions, especially in soils treated with fertilizers. However, few researchers have studied how forest soils respond to nutrient additions, so we are not sure how the potential nitrification and denitrification activities (PNA and PDA, respectively) and microbial communities involved in these processes might respond when N and P are added to temperate and subtropical forest soils. We investigated how the PNA, PDA, the abundances and community compositions of nitrifiers and denitrifiers, and environmental properties, including soil pH, soil total and dissolved organic carbon, total and available N and phosphorus P, changed when N and/or P were added to subtropical and temperate forest soils. We quantified the abundance, and analyzed the composition, of functional marker genes of nitrifiers (ammonia-oxidizing bacteria and archaea amoA) and denitrifiers (nirK and nirS) using quantitative PCR and sequencing, respectively. We found that the PNA and PDA in the subtropical soil increased when P was added and PNA in the temperate forest soil increased when either N or P was added. The PNA and PDA were positively correlated with the abundance of ammonia-oxidizing bacteria and nirK-denitrifiers, respectively, in the subtropical forest soil but were not correlated with changes in corresponding community compositions in either of the forest soils. The soil total N to total P ratio explained most of the variabilities in the PNA and PDA in the subtropical forest soils, and the soil exchangeable ammonium concentrations and pH were the main controls on the PNA and PDA, respectively, in the temperate forest soils. Our results indicate that soil environmental conditions have more influence on variations in the PNA and PDA in forest soils fertilized with N and P than the corresponding microbial properties.
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Affiliation(s)
- Yuqian Tang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, Beijing Normal University, Beijing 100875, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Xinyu Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Qiufeng Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Dashuan Tian
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Tian
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Shuli Niu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Jianping Ge
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, Beijing Normal University, Beijing 100875, China
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Wang X, Wang S, Shi G, Wang W, Zhu G. Factors driving the distribution and role of AOA and AOB in Phragmites communis
rhizosphere in riparian zone. J Basic Microbiol 2019; 59:425-436. [DOI: 10.1002/jobm.201800581] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/01/2018] [Accepted: 12/16/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Guoshuai Shi
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing 100049 China
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Zhou X, Li B, Guo Z, Wang Z, Luo J, Lu C. Niche Separation of Ammonia Oxidizers in Mudflat and Agricultural Soils Along the Yangtze River, China. Front Microbiol 2018; 9:3122. [PMID: 30619196 PMCID: PMC6305492 DOI: 10.3389/fmicb.2018.03122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/03/2018] [Indexed: 12/30/2022] Open
Abstract
Nitrification driven by ammonia oxidizers is a key step of nitrogen removal in estuarine environments. Spatial distribution characteristics of ammonia-oxidizers have been well understood in mudflats, but less studied in the agricultural soils next to mudflats, which also play an important role in nitrogen cycling of the estuarine ecosystem. In the present research, we investigated ammonia oxidizers' distributions along the Yangtze River estuary in Jiangsu Province, China, sampling soils right next to the estuary (mudflats) and the agricultural soils 100 m away. We determined the relationship between the abundance of amoA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and the potential nitrification rates of the mudflats and agricultural soils. We also identified the environmental variables that correlated with the composition of the ammonia oxidizers' communities by 16S rRNA gene pyrosequencing. Results indicated that agricultural soils have significantly higher potential nitrification rates as well as the AOA abundance, and resulted in strong phylogenetic clustering only in AOA communities. The ammonia oxidizers' community compositions differed dramatically among the mudflat and agricultural sites, and stochasticity played a dominant role. The AOA communities were dominated by the Group 1.1a cluster at the mudflat, whereas the 54D9 and 29i4 clusters were dominant in agriculture soils. The dominant AOB communities in the mudflat were closely related to the Nitrosospira lineage, whereas the agricultural soils were dominated by the Nitrosomonas lineage. Soil organic matter and salinity were correlated with the ammonia oxidizers' community compositions.
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Affiliation(s)
- Xue Zhou
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Bolun Li
- School of Geographic Sciences, Nanjing University of Information Science and Technology, Nanjing, China
| | - Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhiyuan Wang
- Center for Eco-Environmental Research, Nanjing Hydraulic Research Institute, Nanjing, China
| | - Jian Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Chunhui Lu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
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Xu HJ, Chen H, Wang XL, Zhang YL, Wang JJ, Li N, Li YT. Earthworms stimulate nitrogen transformation in an acidic soil under different Cd contamination. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 165:564-572. [PMID: 30236918 DOI: 10.1016/j.ecoenv.2018.09.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/06/2018] [Accepted: 09/08/2018] [Indexed: 06/08/2023]
Abstract
In acidic Cd-contaminated soils, soil nitrogen conversion is inhibited and usually block nitrogen supply for plants. Earthworms are well known for improving soil properties and regulating various soil biogeochemical processes including nitrogen cycling. To figure out the effect and mechanisms of earthworms on soil nitrogen transformation in Cd-contaminated soil, ten treatments with and without A. robustus in five soil Cd concentration gradients were established. The tolerant concentration of A. robustus to Cd in the acidic soil is about 6 mg kg-1. The potential ammonia oxidation of the acidic soils was very low, ranging from 0.05 to 0.1 µg NO2--N g-1 d-1. Although AOA was more abundant in the acidic soil than AOB, AOA was inhibited by Cd pollution, while AOB showed some increase under Cd-stress. AOA may play a dominant role in ammonia oxidation in acidic soil, but the recovery of nitrification in Cd-contaminated acidic soil was probably due to the effect of AOB. Earthworms significantly increased soil pH, DOC, ammonium and PAO, thus promoted soil ammonification and potential nitrification, but had no significant effect on soil net nitrification. Correlation analysis results demonstrate that earthworms may promote soil PAO by increasing soil pH, NH4+-N content, and AOB abundance. This study could provide a theoretical basis for solving the problem of nitrogen-cycling-functional degradation and nitrogen supply in the process of phytoremediation of heavy metals-contaminated soils.
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Affiliation(s)
- Hui-Juan Xu
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Hao Chen
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xue-Li Wang
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Yu-Long Zhang
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jin-Jin Wang
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Ning Li
- Guangxi Zhuang Autonomous Region Environmental Monitoring Centre, Nanning 530028, China
| | - Yong-Tao Li
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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Ren L, Cai C, Zhang J, Yang Y, Wu G, Luo L, Huang H, Zhou Y, Qin P, Yu M. Key environmental factors to variation of ammonia-oxidizing archaea community and potential ammonia oxidation rate during agricultural waste composting. BIORESOURCE TECHNOLOGY 2018; 270:278-285. [PMID: 30223159 DOI: 10.1016/j.biortech.2018.09.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
In this research, the abundance and structure of AOA amoA gene during agricultural waste composting were determined by quantitative PCR and sequencing techniques, respectively. Pairwise correlations between potential ammonia oxidation (PAO) rate, physicochemical parameters and the AOA abundance were evaluated using Pearson correlation coefficient. Relationships between these parameters, PAO rates and AOA community structure were evaluated by redundancy analysis. Results showed that 22 AOA gene OTUs were divided into the soil/sediment lineage by phylogenetic analyses. Significant positive correlations were obtained between AOA amoA gene abundance and moisture, ammonium, water soluble carbon (WSC) and organic matter (OM), respectively. Redundancy analysis showed OM, pH and nitrate significantly explained the AOA amoA gene structure. Pearson correlation revealed the PAO rate correlated positively to ammonium, AOA amoA gene abundance. These results indicated that AOA communities sense the fluctuations in surrounding environment, and ultimately react and influence the nitrogen transformation during agricultural waste composting.
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Affiliation(s)
- Liheng Ren
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; International Joint Laboratory of Hunan Agricultural Typical Pollution Restoration and Water Resources Safety Utilization, Changsha 410128, China
| | - Changqing Cai
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; International Joint Laboratory of Hunan Agricultural Typical Pollution Restoration and Water Resources Safety Utilization, Changsha 410128, China
| | - Jiachao Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; International Joint Laboratory of Hunan Agricultural Typical Pollution Restoration and Water Resources Safety Utilization, Changsha 410128, China.
| | - Yuan Yang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; International Joint Laboratory of Hunan Agricultural Typical Pollution Restoration and Water Resources Safety Utilization, Changsha 410128, China
| | - Genyi Wu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; International Joint Laboratory of Hunan Agricultural Typical Pollution Restoration and Water Resources Safety Utilization, Changsha 410128, China
| | - Lin Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; International Joint Laboratory of Hunan Agricultural Typical Pollution Restoration and Water Resources Safety Utilization, Changsha 410128, China
| | - Hongli Huang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; International Joint Laboratory of Hunan Agricultural Typical Pollution Restoration and Water Resources Safety Utilization, Changsha 410128, China
| | - Yaoyu Zhou
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; International Joint Laboratory of Hunan Agricultural Typical Pollution Restoration and Water Resources Safety Utilization, Changsha 410128, China
| | - Pufeng Qin
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; International Joint Laboratory of Hunan Agricultural Typical Pollution Restoration and Water Resources Safety Utilization, Changsha 410128, China
| | - Man Yu
- Environmental Resources and Soil Fertilizer Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Wu Z, Zhang X, Dong Y, Xu X, Xiong Z. Microbial explanations for field-aged biochar mitigating greenhouse gas emissions during a rice-growing season. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:31307-31317. [PMID: 30194577 DOI: 10.1007/s11356-018-3112-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Knowledge about the impacts of fresh and field-aged biochar amendments on greenhouse gas (CH4, N2O) emissions is limited. A field experiment was initiated in 2012 to study the effects of fresh and field-aged biochar additions on CH4 and N2O emissions and the associated microbial activity during the entire rice-growing season in typical rice-wheat rotation system in Southeast China. CH4 and N2O fluxes were monitored, and the abundance of methanogen (mcrA), methanotrophy (pmoA), ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), nitrite reductase (nirS, nirK), N2O reductase (nosZ), and potential soil enzyme activities related to CH4 and N2O were simultaneously measured throughout different rice developmental stages. There were three treatments: control (urea without biochar), fresh BC (urea with fresh biochar added in 2015), and aged BC (urea with 3-year field-aged biochar added in 2012). Results showed that field-aged biochar significantly decreased seasonal CH4 emissions by 16.8% in relation to the fresh biochar, though no significant differences were detected between biochars and control treatment. The structural equation model indicated that soil pH, microbial biomass carbon (MBC), pmoA, and mcrA were the main factors directly influenced by fresh and aged biochar amendments; aged biochar showed a negative effect while fresh biochar showed positive effects on CH4 fluxes. Both fresh and field-aged biochar obviously increased AOA and AOB abundances and reduced the (nirS+nirK)/nosZ ratio during the entire rice-growing season, although no significant effects were observed on seasonal N2O emissions. Therefore, biochar amendment produced long-term effects on total CH4 and N2O emissions through observed influences of soil pH and functional gene abundance. The figure shows how fresh and field-aged biochar differentially affected CH4 production and oxidation and N2O production and reduction through related functional gene abundances. Blue arrows indicate suppressing while pink arrows indicate promoting effect.
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Affiliation(s)
- Zhen Wu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yubing Dong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Xu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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57
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Chase AB, Gomez-Lunar Z, Lopez AE, Li J, Allison SD, Martiny AC, Martiny JBH. Emergence of soil bacterial ecotypes along a climate gradient. Environ Microbiol 2018; 20:4112-4126. [PMID: 30209883 DOI: 10.1111/1462-2920.14405] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/03/2018] [Accepted: 09/06/2018] [Indexed: 11/28/2022]
Abstract
The high diversity of soil bacteria is attributed to the spatial complexity of soil systems, where habitat heterogeneity promotes niche partitioning among bacterial taxa. This premise remains challenging to test, however, as it requires quantifying the traits of closely related soil bacteria and relating these traits to bacterial abundances and geographic distributions. Here, we sought to investigate whether the widespread soil taxon Curtobacterium consists of multiple coexisting ecotypes with differential geographic distributions. We isolated Curtobacterium strains from six sites along a climate gradient and assayed four functional traits that may contribute to niche partitioning in leaf litter, the top layer of soil. Our results revealed that cultured isolates separated into fine-scale genetic clusters that reflected distinct suites of phenotypic traits, denoting the existence of multiple ecotypes. We then quantified the distribution of Curtobacterium by analysing metagenomic data collected across the gradient over 18 months. Six abundant ecotypes were observed with differential abundances along the gradient, suggesting fine-scale niche partitioning. However, we could not clearly explain observed geographic distributions of ecotypes by relating their traits to environmental variables. Thus, while we can resolve soil bacterial ecotypes, the traits delineating their distinct niches in the environment remain unclear.
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Affiliation(s)
- Alexander B Chase
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Zulema Gomez-Lunar
- Department of Earth System Sciences, University of California, Irvine, California, USA
| | - Alberto E Lopez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Junhui Li
- Department of Earth System Sciences, University of California, Irvine, California, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA.,Department of Earth System Sciences, University of California, Irvine, California, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA.,Department of Earth System Sciences, University of California, Irvine, California, USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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58
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Bardon C, Misery B, Piola F, Poly F, Le Roux X. Control of soil N cycle processes byPteridium aquilinumandErica cinereain heathlands along a pH gradient. Ecosphere 2018. [DOI: 10.1002/ecs2.2426] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Clément Bardon
- Microbial Ecology Centre; INRA; CNRS; UMR INRA 1418; UMR CNRS 5557; Université Lyon 1; Université de Lyon; Villeurbanne Cedex F-69622 France
- LEHNA; UMR CNRS 5023; ENTPE; Université Lyon 1; Université de Lyon; Villeurbanne Cedex F-69622 France
| | - Boris Misery
- Microbial Ecology Centre; INRA; CNRS; UMR INRA 1418; UMR CNRS 5557; Université Lyon 1; Université de Lyon; Villeurbanne Cedex F-69622 France
| | - Florence Piola
- LEHNA; UMR CNRS 5023; ENTPE; Université Lyon 1; Université de Lyon; Villeurbanne Cedex F-69622 France
| | - Franck Poly
- Microbial Ecology Centre; INRA; CNRS; UMR INRA 1418; UMR CNRS 5557; Université Lyon 1; Université de Lyon; Villeurbanne Cedex F-69622 France
| | - Xavier Le Roux
- Microbial Ecology Centre; INRA; CNRS; UMR INRA 1418; UMR CNRS 5557; Université Lyon 1; Université de Lyon; Villeurbanne Cedex F-69622 France
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Ammonia-Oxidizing Archaea (AOA) Play with Ammonia-Oxidizing Bacteria (AOB) in Nitrogen Removal from Wastewater. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2018; 2018:8429145. [PMID: 30302054 PMCID: PMC6158934 DOI: 10.1155/2018/8429145] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2022]
Abstract
An increase in the number of publications in recent years indicates that besides ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal from wastewater, gaining wide attention in the wastewater engineering field. This paper reviews the current knowledge on AOA and AOB involved in wastewater treatment systems and summarises the environmental factors affecting AOA and AOB. Current findings reveal that AOA have stronger environmental adaptability compared with AOB under extreme environmental conditions (such as low temperature and low oxygen level). However, there is still little information on the cooperation and competition relationship between AOA and AOB, and other microbes related to nitrogen removal, which needs further exploration. Furthermore, future studies are proposed to develop novel nitrogen removal processes dominated by AOA by parameter optimization.
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Wu Y, Li Y, Fu X, Shen J, Chen D, Wang Y, Liu X, Xiao R, Wei W, Wu J. Effect of controlled-release fertilizer on N 2O emissions and tea yield from a tea field in subtropical central China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:25580-25590. [PMID: 29959739 DOI: 10.1007/s11356-018-2646-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Abstract
Tea (Camellia sinensis L.), a perennial leaf-harvested crop, favors warm/humid climate and acidic/well-drained soils, and demands high nitrogen (N) fertilizer inputs which lead to significant emissions of N2O. Potential mitigation options should be adopted to improve N use efficiency (NUE) and reduce environmental pollution in tea field system. A 3-year field experiment was carried out in a tea field in southern China from January 2014 to December 2016 to investigate the effect of controlled-release fertilizer (CRF) application on N2O emissions in tea field system. Three practices, namely conventional treatment (CON, 105 kg N-oilcake ha-1 year-1 + 345 kg N-urea ha-1 year-1), treatment with a half amount of the N fertilizer (CRF50%, 105 kg N-oilcake ha-1 year-1 + 120 kg N CRF ha-1 year-1) and full amount of N fertilizer (CRF100%, 105 kg N-oilcake ha-1 year-1 + 345 kg N CRF ha-1 year-1) were used. Compared with the CON, our results showed that CRF50% reduced the N2O emissions by 26.2% (p > 0.05) and increased the tea yield by 31.3% (p > 0.05), while CRF100% significantly increased the N2O emissions by 96.7% (p < 0.05) and decreased the tea yield by 6.77% (p > 0.05). Overall, yield-scaled N2O emissions of tea were reduced by 44.5% (p > 0.05) under CRF50% and significantly increased by 100% (p < 0.05) under CRF100%, compared with CON. Based on the gross margin analysis, CRF50% obtained the highest net economic profit. Our findings suggest that reducing N input of CRF (CRF50%) is necessary and feasible for adoption in the current tea plantation system.
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Affiliation(s)
- Yanzheng Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Yong Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.
| | - Xiaoqing Fu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Jianlin Shen
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.
| | - Dan Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Yi Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Xinliang Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Runlin Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Wenxue Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
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Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization. Appl Environ Microbiol 2018; 84:AEM.01031-18. [PMID: 30006397 DOI: 10.1128/aem.01031-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/04/2018] [Indexed: 11/20/2022] Open
Abstract
Long-term effects of inorganic and organic fertilization on nitrification activity (NA) and the abundances and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated in an acidic Ultisol. Seven treatments applied annually for 27 years comprised no fertilization (control), inorganic NPK fertilizer (N), inorganic NPK fertilizer plus lime (CaCO3) (NL), inorganic NPK fertilizer plus peanut straw (NPS), inorganic NPK fertilizer plus rice straw (NRS), inorganic NPK fertilizer plus radish (NR), and inorganic NPK fertilizer plus pig manure (NPM). In nonfertilized soil, the abundance of AOA was 1 order of magnitude higher than that of AOB. Fertilization reduced the abundance of AOA but increased that of AOB, especially in the NL treatment. The AOA communities in the control and the N treatments were dominated by the Nitrososphaera and B1 clades but shifted to clade A in the NL and NPM treatments. Nitrosospira cluster 8a was found to be the most dominant AOB in all treatments. NA was primarily regulated by soil properties, especially soil pH, and the interaction with AOB abundance explained up to 73% of the variance in NA. When NL soils with neutral pH were excluded from the analysis, AOB abundance, especially the relative abundance of Nitrosospira cluster 8a, was positively associated with NA. In contrast, there was no association between AOA abundance and NA. Overall, our data suggest that Nitrosospira cluster 8a of AOB played an important role in the nitrification process in acidic soil following long-term inorganic and organic fertilization.IMPORTANCE The nitrification process is an important step in the nitrogen (N) cycle, affecting N availability and N losses to the wider environment. Ammonia oxidation, which is the first and rate-limiting step of nitrification, was widely accepted to be mainly regulated by AOA in acidic soils. However, in this study, nitrification activity was correlated with the abundance of AOB rather than that of AOA in acidic Ultisols. Nitrosospira cluster 8a, a phylotype of AOB which preferred warm temperatures, and low soil pH played a predominant role in the nitrification process in the test Ultisols. Our results also showed that long-term application of lime or pig manure rather than plant residues altered the community structure of AOA and AOB. Taken together, our findings contribute new knowledge to the understanding of the nitrification process and ammonia oxidizers in subtropical acidic Ultisol under long-term inorganic and organic fertilization.
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Soper FM, Sullivan BW, Nasto MK, Osborne BB, Bru D, Balzotti CS, Taylor PG, Asner GP, Townsend AR, Philippot L, Porder S, Cleveland CC. Remotely sensed canopy nitrogen correlates with nitrous oxide emissions in a lowland tropical rainforest. Ecology 2018; 99:2080-2089. [DOI: 10.1002/ecy.2434] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/23/2018] [Accepted: 06/11/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Fiona M. Soper
- Department of Ecosystem and Conservation Sciences University of Montana Missoula Montana 59808 USA
| | - Benjamin W. Sullivan
- Department of Natural Resources and Environmental Science University of Nevada Reno Nevada 89557 USA
| | - Megan K. Nasto
- Department of Biology, and the Ecology Center Utah State University Logan Utah 84322 USA
| | - Brooke B. Osborne
- Department of Ecology and Evolutionary Biology Brown University Providence Rhode Island 02912 USA
| | - David Bru
- INRA UMR 1347 Agroécologie Dijon France
| | - Christopher S. Balzotti
- Department of Global Ecology Carnegie Institution for Science 206 Panama Street Stanford California 94305 USA
| | - Phillip G. Taylor
- The Institute of Arctic and Alpine Research University of Colorado Boulder Colorado 80303 USA
| | - Gregory P. Asner
- Department of Global Ecology Carnegie Institution for Science 206 Panama Street Stanford California 94305 USA
| | - Alan R. Townsend
- The Institute of Arctic and Alpine Research University of Colorado Boulder Colorado 80303 USA
| | | | - Stephen Porder
- Department of Ecology and Evolutionary Biology Brown University Providence Rhode Island 02912 USA
| | - Cory C. Cleveland
- Department of Ecosystem and Conservation Sciences University of Montana Missoula Montana 59808 USA
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63
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Meinhardt KA, Stopnisek N, Pannu MW, Strand SE, Fransen SC, Casciotti KL, Stahl DA. Ammonia‐oxidizing bacteria are the primary N2O producers in an ammonia‐oxidizing archaea dominated alkaline agricultural soil. Environ Microbiol 2018; 20:2195-2206. [DOI: 10.1111/1462-2920.14246] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/11/2018] [Accepted: 04/15/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Kelley A. Meinhardt
- Department of Civil and Environmental EngineeringUniversity of WashingtonSeattle Washington USA
| | - Nejc Stopnisek
- Department of Civil and Environmental EngineeringUniversity of WashingtonSeattle Washington USA
| | - Manmeet W. Pannu
- Department of Civil and Environmental EngineeringUniversity of WashingtonSeattle Washington USA
| | - Stuart E. Strand
- Department of Civil and Environmental EngineeringUniversity of WashingtonSeattle Washington USA
| | - Steven C. Fransen
- Department of Crop and Soil SciencesWashington State UniversityProsser Washington USA
| | - Karen L. Casciotti
- Department of Earth System ScienceStanford UniversityStanford California USA
| | - David A. Stahl
- Department of Civil and Environmental EngineeringUniversity of WashingtonSeattle Washington USA
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64
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Zhang LM, Duff AM, Smith CJ. Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems. Environ Microbiol 2018; 20:2834-2853. [DOI: 10.1111/1462-2920.14238] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/01/2018] [Accepted: 04/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Li-Mei Zhang
- Microbiology, School of Natural Sciences; NUI Galway, University Road; Galway Ireland
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Science, Chinese Academy of Sciences, 18 Shuangqing Rd.; Haidan Beijing 100085 P.R. China
| | - Aoife M. Duff
- Microbiology, School of Natural Sciences; NUI Galway, University Road; Galway Ireland
| | - Cindy J. Smith
- Microbiology, School of Natural Sciences; NUI Galway, University Road; Galway Ireland
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65
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Guardia G, Marsden KA, Vallejo A, Jones DL, Chadwick DR. Determining the influence of environmental and edaphic factors on the fate of the nitrification inhibitors DCD and DMPP in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:1202-1212. [PMID: 29929233 DOI: 10.1016/j.scitotenv.2017.12.250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 05/25/2023]
Abstract
Nitrification inhibitors (NIs) such as dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) provide an opportunity to reduce losses of reactive nitrogen (Nr) from agricultural ecosystems. To understand the fate and efficacy of these two inhibitors, laboratory-scale experiments were conducted with 14C-labelled DCD and DMPP to determine the relative rates of mineralization, recovery in soil extracts and sorption in two agricultural soils with contrasting pH and organic matter content. Concurrently, the net production of soil ammonium and nitrate in soil were determined. Two months after NI addition to soil, significantly greater mineralization of 14C-DMPP (15.3%) was observed, relative to that of 14C-DCD (10.7%), and the mineralization of both NIs increased with temperature, regardless of NI and soil type. However, the mineralization of NIs did not appear to have a major influence on their inhibitory effect (as shown by the low mineralization rates and the divergent average half-lives for mineralization and nitrification, which were 454 and 37days, respectively). The nitrification inhibition efficacy of DMPP was more dependent on soil type than that of DCD, although the efficacy of both inhibitors was lower in the more alkaline, low-organic matter soil. Although a greater proportion of DMPP becomes unavailable, possibly due to physico-chemical sorption to soil or microbial immobilization, our results demonstrate the potential of DMPP to achieve higher inhibition rates than DCD in grassland soils. Greater consideration of the interactions between NI type, soil and temperature is required to provide robust and cost-effective advice to farmers on NI use.
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Affiliation(s)
- Guillermo Guardia
- ETSI Agronómica, Alimentaria y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid (UPM), Ciudad Universitaria, 28040 Madrid, Spain.
| | - Karina A Marsden
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Antonio Vallejo
- ETSI Agronómica, Alimentaria y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid (UPM), Ciudad Universitaria, 28040 Madrid, Spain
| | - Davey L Jones
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - David R Chadwick
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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66
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Iwaoka C, Imada S, Taniguchi T, Du S, Yamanaka N, Tateno R. The Impacts of Soil Fertility and Salinity on Soil Nitrogen Dynamics Mediated by the Soil Microbial Community Beneath the Halophytic Shrub Tamarisk. MICROBIAL ECOLOGY 2018; 75:985-996. [PMID: 29032430 DOI: 10.1007/s00248-017-1090-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Nitrogen (N) is one of the most common limiting nutrients for primary production in terrestrial ecosystems. Soil microbes transform organic N into inorganic N, which is available to plants, but soil microbe activity in drylands is sometimes critically suppressed by environmental factors, such as low soil substrate availability or high salinity. Tamarisk (Tamarix spp.) is a halophytic shrub species that is widely distributed in the drylands of China; it produces litter enriched in nutrients and salts that are thought to increase soil fertility and salinity under its crown. To elucidate the effects of tamarisks on the soil microbial community, and thus N dynamics, by creating "islands of fertility" and "islands of salinity," we collected soil samples from under tamarisk crowns and adjacent barren areas at three habitats in the summer and fall. We analyzed soil physicochemical properties, inorganic N dynamics, and prokaryotic community abundance and composition. In soils sampled beneath tamarisks, the N mineralization rate was significantly higher, and the prokaryotic community structure was significantly different, from soils sampled in barren areas, irrespective of site and season. Tamarisks provided suitable nutrient conditions for one of the important decomposers in the area, Verrucomicrobia, by creating "islands of fertility," but provided unsuitable salinity conditions for other important decomposers, Flavobacteria, Gammaproteobacteria, and Deltaproteobacteria, by mitigating salt accumulation. However, the quantity of these decomposers tended to be higher beneath tamarisks, because they were relatively unaffected by the small salinity gradient created by the tamarisks, which may explain the higher N mineralization rate beneath tamarisks.
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Affiliation(s)
- Chikae Iwaoka
- Graduate School of Agriculture, Kyoto University, Oiwake, Kitashirakawa, Sakyo, Kyoto, 606-8502, Japan.
| | - Shogo Imada
- Field Science Education and Research Center, Kyoto University, Kyoto, 606-8502, Japan
- Institute for Environmental Sciences, 1-7 Ienomae, Obuchi, Rokkasho, Kamikita, Aomori, 039-3212, Japan
| | - Takeshi Taniguchi
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - Sheng Du
- State Key Laboratory of Soil Erosion and Dryland Farming on Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Yangling, Shaanxi, 712100, China
| | - Norikazu Yamanaka
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - Ryunosuke Tateno
- Field Science Education and Research Center, Kyoto University, Kyoto, 606-8502, Japan
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67
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Abdala DB, Moore PA, Rodrigues M, Herrera WF, Pavinato PS. Long-term effects of alum-treated litter, untreated litter and NH 4NO 3 application on phosphorus speciation, distribution and reactivity in soils using K-edge XANES and chemical fractionation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 213:206-216. [PMID: 29500994 DOI: 10.1016/j.jenvman.2018.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/24/2018] [Accepted: 02/01/2018] [Indexed: 06/08/2023]
Abstract
Whereas soil test information on the fertility and chemistry of soils has been important to elaborate safe and sound agricultural practices, micro-scale information can give a whole extra dimension to understand the chemical processes occurring in soils. The objective of this study was to evaluate the effects that the consecutive application of untreated poultry litter, alum-treated litter or ammonium nitrate (NH4NO3) had on P solubility in soils over 20 years. For this, we used soil test data, sequential chemical fractionation (SCF) of P, and P K-edge XANES and μ-fluorescence spectroscopies. Water extractable P data indicated that application of alum to poultry litter was a very effective treatment for reducing P solubility. On the basis of our SCF of P data, P was primarily found within the 0.1 M NaOH pool across the applied rates and regardless of the treatment, where application of alum-treated litter accounted for as much as 59 ± 2% of the total, followed by NH4NO3, 49 ± 4%, and untreated litter, 40 ± 2%. It was also shown that in soils where alum-treated litter was applied, the Resin pool accounted for 10 ± 1% of the total, followed by NH4NO3, 13 ± 4%, and untreated litter, 18 ± 2%, indicating that P was less readily available in soils where alum-treated litter was applied. Phosphorus XANES indicated that P was predominantly associated to Fe > Al > Ca > organic molecules, regardless of the treatment or applied rates, though the formation of PoAl complexes was only found in soils that received application of alum-treated litter and was positively related to the applied rates. The combination of P-XANES with SCF or μ-fluorescence data was shown to provide valuable information about P reactivity and distribution in soils and should thus be used to address the fate of applied P amendments in soils.
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Affiliation(s)
- D B Abdala
- Brazilian Synchrotron Light Laboratory, Campinas, São Paulo, 13083-100, Brazil.
| | - P A Moore
- USDA/ARS, Poultry Production and Product Safety Research Unit, Plant Sciences 115, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - M Rodrigues
- Department of Soil Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - W F Herrera
- Department of Soil Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - P S Pavinato
- Department of Soil Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
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68
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Effects of reforestation on ammonia-oxidizing microbial community composition and abundance in subtropical acidic forest soils. Appl Microbiol Biotechnol 2018; 102:5309-5322. [DOI: 10.1007/s00253-018-8873-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 02/03/2018] [Accepted: 02/10/2018] [Indexed: 01/01/2023]
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69
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He L, Bi Y, Zhao J, Pittelkow CM, Zhao X, Wang S, Xing G. Population and community structure shifts of ammonia oxidizers after four-year successive biochar application to agricultural acidic and alkaline soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:1105-1115. [PMID: 29734589 DOI: 10.1016/j.scitotenv.2017.11.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 06/08/2023]
Abstract
Long-term studies that advance our mechanistic understanding of biochar (BC)‑nitrogen (N) interactions in agricultural soils are lacking. In this study, soil potential nitrification rates (PNR), the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities following 4-year of BC application were investigated using the shaken-slurry procedure and molecular sequencing techniques for an acidic Oxisol (QU) and an alkaline Cambisol (YU). Soils were obtained from an outdoor soil column experiment with straw-BC application rates of 0 (BC0), 2.25 (BC2.25) and 11.3 (BC11.3) Mgha-1 per cropping season for eight consecutive wheat/millet seasons. Quantitative polymerase chain reaction (qPCR) and 454 high-throughput pyrosequencing techniques were performed to quantify and sequence amoA gene copies and composition of AOA and AOB. Results showed that QU had lower PNR and a higher ratio of amoA gene copies of AOA to AOB than YU, PNR of QU with BC application was significantly associated with the amoA gene of AOB. Similar to previous short-term findings, BC application enhanced QU soil nitrification, which may be explained by the significant increase in AOB abundance and a shift in AOB community structure from Nitrosospira cluster 2 toward cluster 3, along with the disappearance of some obligate acidophile AOA groups, leading to the appearance of ammonia-oxidizers from neutral-alkaline soils in BC-amended acid soils. Canonical correspondence analysis (CCA) showed that soil pH was the most important factor driving shifts in ammonia-oxidizers composition. Although BC application did not have significant effects on PNR in YU, BC11.3 decreased AOA and AOB gene copies and influenced the relative abundance of community structure. Our findings represent the first investigation of long-term BC effects on AOA and AOB communities in agricultural soils using 454 high-throughput pyrosequencing, showing that BC application can alter soil characteristics and influence ammonia oxidizer community composition, abundance, especially in acid soils.
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Affiliation(s)
- Lili He
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou 310021, China
| | - Yucui Bi
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jin Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | | | - Xu Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Shenqiang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Guangxi Xing
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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70
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Liu J, Yu Z, Yao Q, Sui Y, Shi Y, Chu H, Tang C, Franks AE, Jin J, Liu X, Wang G. Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China. Front Microbiol 2018; 9:171. [PMID: 29497404 PMCID: PMC5819564 DOI: 10.3389/fmicb.2018.00171] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/25/2018] [Indexed: 11/13/2022] Open
Abstract
Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.
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Affiliation(s)
- Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, AgriBio Centre for AgriBiosciences, La Trobe University, Bundoora VIC, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora VIC, Australia
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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71
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He H, Zhen Y, Mi T, Fu L, Yu Z. Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China. Front Microbiol 2018; 9:116. [PMID: 29456526 PMCID: PMC5801408 DOI: 10.3389/fmicb.2018.00116] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/18/2018] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA) gene. Molecular biology techniques were used to analyze ammonia oxidizers’ community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers’ community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla) and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.
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Affiliation(s)
- Hui He
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Lulu Fu
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, China
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72
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Yao L, Chen C, Liu G, Li F, Liu W. Environmental factors, but not abundance and diversity of nitrifying microorganisms, explain sediment nitrification rates in Yangtze lakes. RSC Adv 2018; 8:1875-1883. [PMID: 35542587 PMCID: PMC9077250 DOI: 10.1039/c7ra11956a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/28/2017] [Indexed: 11/21/2022] Open
Abstract
Sediment nitrification plays a vital role in nitrogen (N) biogeochemical cycling and ecological function of an aquatic ecosystem.
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Affiliation(s)
- Lu Yao
- Key Laboratory of Aquatic Botany and Watershed Ecology
- Wuhan Botanical Garden
- Chinese Academy of Sciences
- Wuhan
- PR China
| | - Chengrong Chen
- Australian Rivers Institute and Griffith School of Environment
- Griffith University
- Nathan
- Australia
| | - Guihua Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology
- Wuhan Botanical Garden
- Chinese Academy of Sciences
- Wuhan
- PR China
| | - Feng Li
- Dongting Lake Station for Wetland Ecosystem Research
- Institute of Subtropical Agriculture
- The Chinese Academy of Sciences
- Changsha 410125
- PR China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology
- Wuhan Botanical Garden
- Chinese Academy of Sciences
- Wuhan
- PR China
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Awasthi MK, Wang Q, Awasthi SK, Wang M, Chen H, Ren X, Zhao J, Zhang Z. Influence of medical stone amendment on gaseous emissions, microbial biomass and abundance of ammonia oxidizing bacteria genes during biosolids composting. BIORESOURCE TECHNOLOGY 2018; 247:970-979. [PMID: 30060437 DOI: 10.1016/j.biortech.2017.09.201] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/26/2017] [Accepted: 09/28/2017] [Indexed: 06/08/2023]
Abstract
This study aimed to evaluate the feasibility of medical stone (MS) on microbial biomass, bacteria genes copy numbers, mitigation of gaseous emissions and its correlation with analyzed parameters during the biosolids composting. Composting of the biosolids by amendment of MS 0%, 2%, 4%, 6% and 10% (on dry weight basis) was performed using a 130-L composting reactor. The results showed that with increasing the dosage of MS, the CH4, N2O and NH3 emission were reduced by 60.5-88.3%, 46.6-82.4% and 38.2-78.5%, respectively. In addition, the 6-10% MS amendment enhanced the organic waste mineralization and prolonged the thermophilic phase. The abundance of ammonia oxidizing bacteria (AOB) and archaea (AOAB) were decreased during the first 28 days, but considerable increment was observed during the maturation phase which indicated that AOB and AOAB were liable for nitrification during the curing phase of composting. A significant correlation was observed among the all analyzed parameters in 6-10% MS blended treatments.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Department of Biotechnology, Amicable Knowledge Solution University, Satna, India
| | - Quan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Meijing Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Hongyu Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Xiuna Ren
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Junchao Zhao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China.
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74
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Wang SP, Zhong XZ, Wang TT, Sun ZY, Tang YQ, Kida K. Aerobic composting of distilled grain waste eluted from a Chinese spirit-making process: The effects of initial pH adjustment. BIORESOURCE TECHNOLOGY 2017; 245:778-785. [PMID: 28926909 DOI: 10.1016/j.biortech.2017.09.051] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
Aerobic composting of distilled grain waste (DGW) at different initial pH values adjusted by CaO addition was investigated. Three pH-adjusted treatments with initial pH values of 4 (R1), 5 (R2) and 6 (R3) and a control treatment (R0) with a pH value of 3.5 were conducted simultaneously. The results showed that R0 had an unsuccessful start-up of composting. However, the pH-adjusted treatments produced remarkable results, with a relatively high initial pH being beneficial for the start-up. Within 65days of composting, the degradation of volatile solids (VS) and the physicochemical properties of R2 and R3 displayed similar tendencies, and both produced a mature end-product, while R1 exhibited a lower VS degradation rate, and some of its physicochemical properties indicated the end-product was immature. Quantitative PCR analysis of ammonia oxidizers indicated that the occurrence of nitrification during the composting of DGW could be attributed to the activity of ammonia-oxidizing bacteria.
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Affiliation(s)
- Shi-Peng Wang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu 610065, Sichuan, China
| | - Xiao-Zhong Zhong
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu 610065, Sichuan, China
| | - Ting-Ting Wang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu 610065, Sichuan, China
| | - Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu 610065, Sichuan, China.
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu 610065, Sichuan, China
| | - Kenji Kida
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu 610065, Sichuan, China
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75
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Yang W, Wang Y, Tago K, Tokuda S, Hayatsu M. Comparison of the Effects of Phenylhydrazine Hydrochloride and Dicyandiamide on Ammonia-Oxidizing Bacteria and Archaea in Andosols. Front Microbiol 2017; 8:2226. [PMID: 29184545 PMCID: PMC5694480 DOI: 10.3389/fmicb.2017.02226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/30/2017] [Indexed: 11/13/2022] Open
Abstract
Dicyandiamide, a routinely used commercial nitrification inhibitor (NI), inhibits ammonia oxidation catalyzed by ammonia monooxygenase (AMO). Phenylhydrazine hydrochloride has shown considerable potential for the development of next-generation NIs targeting hydroxylamine dehydrogenase (HAO). The effects of the AMO inhibitor and the HAO inhibitor on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) present in agricultural soils have not been compared thus far. In the present study, the effects of the two inhibitors on soil nitrification and the abundance of AOA and AOB as well as their community structure were investigated in a soil microcosm using quantitative polymerase chain reaction and pyrosequencing. The net nitrification rates and the growth of AOA and AOB in this soil microcosm were inhibited by both NIs. Both NIs had limited effect on the community structure of AOB and no effect on that of AOA in this soil microcosm. The effects of phenylhydrazine hydrochloride were similar to those of dicyandiamide. These results indicated that organohydrazine-based NIs have potential for the development of next-generation NIs targeting HAO in the future.
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Affiliation(s)
- Wenjie Yang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, China
| | - Yong Wang
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kanako Tago
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Shinichi Tokuda
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Kyoto, Japan
| | - Masahito Hayatsu
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
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76
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Xi R, Long XE, Huang S, Yao H. pH rather than nitrification and urease inhibitors determines the community of ammonia oxidizers in a vegetable soil. AMB Express 2017. [PMID: 28641404 PMCID: PMC5479772 DOI: 10.1186/s13568-017-0426-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Nitrification inhibitors and urease inhibitors, such as nitrapyrin and N-(n-butyl) thiophosphoric triamide (NBPT), can improve the efficiencies of nitrogen fertilizers in cropland. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across different soil pH levels are still unclear. In the present work, vegetable soils at four pH levels were tested to determine the impacts of nitrification and urease inhibitors on the nitrification activities, abundances and diversities of ammonia oxidizers at different pHs by real-time PCR, terminal restriction fragment length polymorphism (T-RFLP) and clone sequence analysis. The analyses of the abundance of ammonia oxidizers and net nitrification rate suggested that AOA was the dominate ammonia oxidizer and the key driver of nitrification in acidic soil. The relationships between pH and ammonia oxidizer abundance indicated that soil pH dominantly controlled the abundance of AOA but not that of AOB. The T-RFLP results suggested that soil pH could significantly affect the AOA and AOB community structure. Nitrapyrin decreased the net nitrification rate and inhibited the abundance of bacterial amoA genes in this vegetable soil, but exhibited no effect on that of the archaeal amoA genes. In contrast, NBPT just lagged the hydrolysis of urea and kept low NH4+-N levels in the soil at the early stage. It exhibited no or slight effects on the abundance and community structure of ammonia oxidizers. These results indicated that soil pH, rather than the application of urea, nitrapyrin and NBPT, was a critical factor influencing the abundance and community structure of AOA and AOB.
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77
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Wu RN, Meng H, Wang YF, Lan W, Gu JD. A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils. MICROBIAL ECOLOGY 2017; 74:910-922. [PMID: 28808742 DOI: 10.1007/s00248-017-1045-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/13/2017] [Indexed: 05/20/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al3+ species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH3/NH4+ equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al3+. Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils.
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Affiliation(s)
- Ruo-Nan Wu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Han Meng
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Yong-Feng Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, People's Republic of China
- Laboratory of Microbial Ecology and Toxicology, Guangdong Academy of Forestry, Guangzhou, People's Republic of China
| | - Wensheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.
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78
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Jiang X, Wu Y, Liu G, Liu W, Lu B. The effects of climate, catchment land use and local factors on the abundance and community structure of sediment ammonia-oxidizing microorganisms in Yangtze lakes. AMB Express 2017; 7:173. [PMID: 28905318 PMCID: PMC5597559 DOI: 10.1186/s13568-017-0479-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/05/2017] [Indexed: 11/30/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in regulating the nitrification process in lake ecosystems. However, the relative effects of climate, catchment land use and local conditions on the sediment ammonia-oxidizing communities in lakes remain unclear. In this study, the diversity and abundance of AOA and AOB communities were investigated in ten Yangtze lakes by polymerase chain reaction (PCR), clone library and quantitative PCR techniques. The results showed that the abundances of both AOA and AOB in bare sediments were considerably but not significantly higher than those in vegetated sediments. Interestingly, AOB communities were more sensitive to changes in local environmental factors and vegetation characteristics than were AOA communities. Amongst climate and land use variables, mean annual precipitation, percentage of agriculture and percentage of vegetation were the key determinants of AOB abundance and diversity. Additionally, total organic carbon and chlorophyll-a concentrations in lake water were significantly related to AOB abundance and diversity. The results of the ordination analysis indicated that 81.2 and 84.3% of the cumulative variance for the species composition of AOA and AOB communities could be explained by the climate, land use and local factors. The climate and local environments played important roles in shaping AOA communities, whereas catchment agriculture and water chlorophyll-a concentration were key influencing factors of AOB communities. Our findings suggest that the composition and structure of sediment ammonia-oxidizing communities in Yangtze lakes are strongly influenced by different spatial scale factors.
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79
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Posmanik R, Nejidat A, Dahan O, Gross A. Seasonal and soil-type dependent emissions of nitrous oxide from irrigated desert soils amended with digested poultry manures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 593-594:91-98. [PMID: 28342421 DOI: 10.1016/j.scitotenv.2017.03.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 06/06/2023]
Abstract
Expansion of dryland agriculture requires intensive supplement of organic fertilizers to improve the fertility of nutrient-poor desert soils. The environmental impact of organic supplements in hot desert climates is not well understood. We report on seasonal emissions of nitrous oxide (N2O) from sand and loess soils, amended with limed and non-limed anaerobic digestate of poultry manure in the Israeli Negev desert. All amended soils had substantially higher N2O emissions, particularly during winter applications, compared to unammended soils. Winter emissions from amended loess (10-175mgN2Om-2day-1) were markedly higher than winter emissions from amended sand (2-7mgN2Om-2day-1). Enumeration of marker genes for nitrification and denitrification suggested that both have contributed to N2O emissions according to prevailing environmental conditions. Lime treatment of digested manure inhibited N2O emissions regardless of season or soil type, thus reducing the environmental impact of amending desert soils with manure digestate.
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Affiliation(s)
- Roy Posmanik
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel
| | - Ali Nejidat
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel.
| | - Ofer Dahan
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel
| | - Amit Gross
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel.
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80
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Wang J, Ni L, Song Y, Rhodes G, Li J, Huang Q, Shen Q. Dynamic Response of Ammonia-Oxidizers to Four Fertilization Regimes across a Wheat-Rice Rotation System. Front Microbiol 2017; 8:630. [PMID: 28446904 PMCID: PMC5388685 DOI: 10.3389/fmicb.2017.00630] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/28/2017] [Indexed: 11/23/2022] Open
Abstract
Ammonia oxidation by microorganisms is a rate-limiting step of the nitrification process and determines the efficiency of fertilizer utilized by crops. Little is known about the dynamic response of ammonia-oxidizers to different fertilization regimes in a wheat-rice rotation system. Here, we examined ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities across eight representative stages of wheat and rice growth and under four fertilization regimes: no nitrogen fertilization (NNF), chemical fertilization (CF), organic-inorganic mixed fertilizer (OIMF) and organic fertilization (OF). The abundance and composition of ammonia oxidizers were analyzed using quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) of their amoA genes. Results showed that fertilization but not plant growth stages was the best predictor of soil AOB community abundance and composition. Soils fertilized with more urea-N had higher AOB abundance, while organic-N input showed little effect on AOB abundance. 109 bp T-RF (Nitrosospira Cluster 3b) and 280 bp T-RF (Nitrosospira Cluster 3c) dominated the AOB communities with opposing responses to fertilization regimes. Although the abundance and composition of the AOA community was significantly impacted by fertilization and plant growth stage, it differed from the AOB community in that there was no particular trend. In addition, across the whole wheat-rice rotation stages, results of multiple stepwise linear regression revealed that AOB played a more important role in ammonia oxidizing process than AOA. This study provided insight into the dynamic effects of fertilization strategies on the abundance and composition of ammonia-oxidizers communities, and also offered insights into the potential of managing nitrogen for sustainable agricultural productivity with respect to soil ammonia-oxidizers.
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Affiliation(s)
- Jichen Wang
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Lei Ni
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Yang Song
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Geoff Rhodes
- Department of Plant, Soil and Microbial Sciences, Michigan State UniversityEast Lansing, MI, USA
| | - Jing Li
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
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81
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Jiang HS, Yin L, Ren NN, Xian L, Zhao S, Li W, Gontero B. The effect of chronic silver nanoparticles on aquatic system in microcosms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 223:395-402. [PMID: 28117183 DOI: 10.1016/j.envpol.2017.01.036] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/13/2017] [Accepted: 01/15/2017] [Indexed: 05/22/2023]
Abstract
Silver nanoparticles (AgNPs) inevitably discharge into aquatic environments due to their abundant use in antibacterial products. It was reported that in laboratory conditions, AgNPs display dose-dependent toxicity to aquatic organisms, such as bacteria, algae, macrophytes, snails and fishes. However, AgNPs could behave differently in natural complex environments. In the present study, a series of microcosms were established to investigate the distribution and toxicity of AgNPs at approximately 500 μg L-1 in aquatic systems. As a comparison, the distribution and toxicity of the same concentration of AgNO3 were also determined. The results showed that the surface layer of sediment was the main sink of Ag element for both AgNPs and AgNO3. Both aquatic plant (Hydrilla verticillata) and animals (Gambusia affinis and Radix spp) significantly accumulated Ag. With short-term treatment, phytoplankton biomass was affected by AgNO3 but not by AgNPs. Chlorophyll content of H. verticillata increased with both AgNPs and AgNO3 short-term exposure. However, the biomass of phytoplankton, aquatic plant and animals was not significantly different between control and samples treated with AgNPs or AgNO3 for 90 d. The communities, diversity and richness of microbes were not significantly affected by AgNPs and AgNO3; in contrast, the nitrification rate and its related microbe (Nitrospira) abundance significantly decreased. AgNPs and AgNO3 may affect the nitrogen cycle and affect the environment and, since they might be also transferred to food web, they represent a risk for health.
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Affiliation(s)
- Hong Sheng Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Aix Marseille Univ CNRS, BIP UMR 7281, IMM, FR 3479, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Liyan Yin
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Agricultural College, Hainan University, Haikou, 570228, China.
| | - Na Na Ren
- College of Geosciences, China University of Petroleum, Beijing 102249, China
| | - Ling Xian
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suting Zhao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Brigitte Gontero
- Aix Marseille Univ CNRS, BIP UMR 7281, IMM, FR 3479, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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82
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Huang YL, Sun ZY, Zhong XZ, Wang TT, Tan L, Tang YQ, Kida K. Aerobic composting of digested residue eluted from dry methane fermentation to develop a zero-emission process. WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 61:206-212. [PMID: 28089402 DOI: 10.1016/j.wasman.2017.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 12/06/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
Digested residue remained at the end of a process for the production of fuel ethanol and methane from kitchen garbage. To develop a zero-emission process, the compostability of the digested residue was assessed to obtain an added-value fertilizer. Composting of the digested residue by adding matured compost and a bulking agent was performed using a lab-scale composting reactor. The composting process showed that volatile total solid (VTS) degradation mainly occurred during the first 13days, and the highest VTS degradation efficiency was about 27% at the end. The raw material was not suitable as a fertilizer due to its high NH4+ and volatile fatty acids (VFAs) concentration. However, the composting process produced remarkable results; the physicochemical properties indicated that highly matured compost was obtained within 62days of the composting process, and the final N concentration, NO3- concentration, and the germination index (GI) at the end of the composting process was 16.4gkg-1-TS, 9.7gkg-1-TS, and 151%, respectively. Real-time quantitative PCR (qPCR) analysis of ammonia oxidizers indicated that the occurrence of nitrification during the composting of digested residue was attributed to the activity of ammonia-oxidizing bacteria (AOB).
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Affiliation(s)
- Yu-Lian Huang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China.
| | - Xiao-Zhong Zhong
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Ting-Ting Wang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Li Tan
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Kenji Kida
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
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83
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Sauder LA, Albertsen M, Engel K, Schwarz J, Nielsen PH, Wagner M, Neufeld JD. Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system. ISME JOURNAL 2017; 11:1142-1157. [PMID: 28195581 PMCID: PMC5398378 DOI: 10.1038/ismej.2016.192] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 11/10/2016] [Accepted: 11/16/2016] [Indexed: 02/07/2023]
Abstract
Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1–2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown metabolism.
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Affiliation(s)
- Laura A Sauder
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Jasmin Schwarz
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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84
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Wang L, Zheng P, Abbas G, Xing Y, Li W, Wang R, Deng L, Lei Y, Zheng D, Zhang Y. Enrichment and characterization of acid-tolerant nitrifying sludge. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 184:196-203. [PMID: 27712918 DOI: 10.1016/j.jenvman.2016.09.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
Nitrification is an acidifying process that requires the addition of external alkalinity because of the alkaliphilic nature of the most ammonia-oxidizing bacteria. In this study, aerobic activated sludge was used as inoculum in an internal loop air-lift reactor, which resulted in successful enrichment of acid-tolerant nitrifying (ACIN) sludge at pH 6.0 by sequential addition of tea orchard soil suspension. The results showed that ACIN sludge had a remarkable acid tolerant capability with a volumetric ammonia conversion rate of 1.13 kg N m-3 day-1. ACIN sludge showed a higher maximum specific ammonia conversion rate (0.29 g N g-1 VSS day-1) than neutrophilic nitrifying sludge (0.14 g N g-1 VSS day-1) at pH 6.0 and had good resistance against pH fluctuations, with a maximum specific ammonia conversion rate (0.584 g N g-1 VSS day-1) at pH 7.5. Microbial community analysis indicated that the higher abundance of acid tolerant Nitrosospira and ammonia-oxidizing archaea laid a solid foundation for the remarkable acid-tolerant capability of ACIN sludge.
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Affiliation(s)
- Lan Wang
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China.
| | - Ghulam Abbas
- Department of Chemical Engineering, University of Gujrat, Pakistan
| | - Yajuan Xing
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Wei Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Ru Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Liangwei Deng
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
| | - Yunhui Lei
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
| | - Dan Zheng
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
| | - Yunhong Zhang
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, China; Laboratory of Development and Application of Rural Renewable Energy, Chengdu 610041, China
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85
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Wang Q, Zhang LM, Shen JP, Du S, Han LL, He JZ. Effects of dicyandiamide and acetylene on N 2O emissions and ammonia oxidizers in a fluvo-aquic soil applied with urea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:23023-23033. [PMID: 27581050 DOI: 10.1007/s11356-016-7519-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are crucial for N2O emission as they carry out the key step of nitrification. Dicyandiamide (DCD) and acetylene (C2H2) are typical nitrification inhibitors (NIs), while the comparative effects of these NIs on N2O production and ammonia oxidizers' (AOB and AOA) growth are unclear. Four treatments including a control, urea, urea + DCD, and urea + C2H2 were set up to investigate their effect of inhibiting soil nitrification, nitrification-related N2O emission as well as the growth of ammonia oxidizers with a fluvo-aquic soil using microcosms for 28 days. N2O emission and net nitrification rate increased after the application of urea, but were significantly restrained in urea + NI treatments, while C2H2 was more effective in reducing N2O emission and nitrification rate than DCD. The abundance of AOB, which was significantly correlated with N2O emission and net nitrification rate, was more inhibited by C2H2 than DCD. Furthermore, the application of urea in all the soils had little impact on the AOA community, while obvious shifts of AOB community structure were found compared with the control. All AOB sequences fell within Nitrosospira cluster 3, and the AOA community was clustered to group 1.1b. Collectively, it indicated that application of urea combined with NIs (DCD or C2H2) could potentially alter N2O emission, mainly through regulating the growth of AOB but not AOA in this fluvo-aquic soil.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Melbourne School of Land and Environment, The University of Melbourne, Parkville, Victoria, Australia.
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86
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Rughöft S, Herrmann M, Lazar CS, Cesarz S, Levick SR, Trumbore SE, Küsel K. Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa. Front Microbiol 2016; 7:1638. [PMID: 27807431 PMCID: PMC5069293 DOI: 10.3389/fmicb.2016.01638] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/30/2016] [Indexed: 11/13/2022] Open
Abstract
Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20-66%), Chloroflexi (9-29%), and Firmicutes (7-42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43-99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g-1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g-1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our results suggest a strong effect of the savanna soils' nutrient scarcity on all microbial communities, resulting in a distinct community structure that differs markedly from nutrient-rich, temperate grasslands, along with a high relevance of archaeal ammonia oxidation in savanna soils.
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Affiliation(s)
- Saskia Rughöft
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Martina Herrmann
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Cassandre S Lazar
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany; Institute of Biology, Leipzig UniversityLeipzig, Germany
| | - Shaun R Levick
- Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| | - Susan E Trumbore
- Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| | - Kirsten Küsel
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
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87
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Araújo ASF, Lima LM, Santos VM, Schmidt R. Repeated application of composted tannery sludge affects differently soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:19193-19200. [PMID: 27351878 DOI: 10.1007/s11356-016-7115-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/20/2016] [Indexed: 06/06/2023]
Abstract
Repeated application of composted tannery sludge (CTS) changes the soil chemical properties and, consequently, can affect the soil microbial properties. The aim of this study was to evaluate the responses of soil microbial biomass and ammonia-oxidizing organisms to repeated application of CTS. CTS was applied repeatedly during 6 years, and, at the sixth year, the soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms were determined in the soil. The treatments consisted of 0 (without CTS application), 2.5, 5, 10, and 20 t ha(-1) of CTS (dry basis). Soil pH, EC, SOC, total N, and Cr concentration increased with the increase in CTS rate. Soil microbial biomass did not change significantly with the amendment of 2.5 Mg ha(-1), while it decreased at the higher rates. Total and specific enzymes activity responded differently after CTS application. The abundance of bacteria did not change with the 2.5-Mg ha(-1) CTS treatment and decreased after this rate, while the abundance of archaea increased significantly with the 2.5-Mg ha(-1) CTS treatment. Repeated application of different CTS rates for 6 years had different effects on the soil microbial biomass and ammonia-oxidizing organisms as a response to changes in soil chemical properties.
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Affiliation(s)
| | - Luciano Moura Lima
- Soil Quality Laboratory Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Vilma Maria Santos
- Soil Quality Laboratory Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Radomir Schmidt
- Department of Land, Air and Water Resources, University of California, Davis, CA, 95616, USA
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88
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Reisinger AJ, Groffman PM, Rosi-Marshall EJ. Nitrogen-cycling process rates across urban ecosystems. FEMS Microbiol Ecol 2016; 92:fiw198. [DOI: 10.1093/femsec/fiw198] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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89
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Pajares S, Bohannan BJM. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils. Front Microbiol 2016; 7:1045. [PMID: 27468277 PMCID: PMC4932190 DOI: 10.3389/fmicb.2016.01045] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/22/2016] [Indexed: 01/08/2023] Open
Abstract
Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.
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Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoCoyoacán, Mexico
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90
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Wu F, Wang JT, Yang J, Li J, Zheng YM. Does arsenic play an important role in the soil microbial community around a typical arsenic mining area? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 213:949-956. [PMID: 27055093 DOI: 10.1016/j.envpol.2016.03.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/09/2016] [Accepted: 03/21/2016] [Indexed: 05/27/2023]
Abstract
Arsenic (As) can cause serious hazards to human health, especially in mining areas. Soil bacterial communities, which are critical parts of the soil ecosystem, were analyzed directly for soil environmental factors. As a consequence, it is of great significance to understand the ecological risk of arsenic contamination on bacteria, especially at the local scale. In this study, 33 pairs of soil and grain samples were collected from the corn and paddy fields around an arsenic mining area in Shimen County in Hunan Province, China. Significant differences were found between the soil nitrogen, As concentrations, and bacteria activities among these two types of land use. According to the structural equation model (SEM) analysis, compared with other environmental factors, soil As was not the key factor affecting the bacterial community, even when grain As was beyond the threshold of the national food hygiene standards of China. In the corn field, soil pH was the main factor dominating the bacterial richness, composition and grain As. Meanwhile, in the paddy field the soil total nitrogen (TN) and total carbon (TC) were the main factors impacting the bacterial richness, and the bacterial community composition was mainly affected by pH. The interactions between grain As and soil As were weak in the corn field. The bacterial communities played important roles in the food chain risk of As. The local policy of transforming paddy soil to dry land could greatly reduce the health risk of As through the food chain.
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Affiliation(s)
- Fan Wu
- 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
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jun Yang
- Institute of Geographic Science and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jing Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China
| | - Yuan-Ming Zheng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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91
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Song H, Che Z, Cao W, Huang T, Wang J, Dong Z. Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:11964-11974. [PMID: 26961528 DOI: 10.1007/s11356-016-6396-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.
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Affiliation(s)
- He Song
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Zhao Che
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Wenchao Cao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Ting Huang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jingguo Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Dong
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
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92
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Sun ZY, Zhang J, Zhong XZ, Tan L, Tang YQ, Kida K. Production of nitrate-rich compost from the solid fraction of dairy manure by a lab-scale composting system. WASTE MANAGEMENT (NEW YORK, N.Y.) 2016; 51:55-64. [PMID: 26965212 DOI: 10.1016/j.wasman.2016.03.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
In the present study, we developed an efficient composting process for the solid fraction of dairy manure (SFDM) using lab-scale systems. We first evaluated the factors affecting the SFDM composting process using different thermophilic phase durations (TPD, 6 or 3days) and aeration rates (AR, 0.4 or 0.2 lmin(-1)kg(-1)-total solid (TS)). Results indicated that a similar volatile total solid (VTS) degradation efficiency (approximately 60%) was achieved with a TPD of 6 or 3days and an AR of 0.4 l min(-1) kg(-1)-TS (hereafter called higher AR), and a TPD of 3days resulted in less N loss caused by ammonia stripping. N loss was least when AR was decreased to 0.2 l min(-1) kg(-1)-TS (hereafter called lower AR) during the SFDM composting process. However, moisture content (MC) in the composting pile increased at the lower AR because of water production by VTS degradation and less water volatilization. Reduced oxygen availability caused by excess water led to lower VTS degradation efficiency and inhibition of nitrification. Adding sawdust to adjust the C/N ratio and decrease the MC improved nitrification during the composing processes; however, the addition of increasing amounts of sawdust decreased NO3(-) concentration in matured compost. When an improved composting reactor with a condensate removal and collection system was used for the SFDM composting process, the MC of the composting pile was significantly reduced, and nitrification was detected 10-14days earlier. This was attributed to the activity of ammonia-oxidizing bacteria (AOB). Highly matured compost could be generated within 40-50days. The VTS degradation efficiency reached 62.0% and the final N content, NO3(-) concentration, and germination index (GI) at the end of the composting process were 3.3%, 15.5×10(3)mg kg(-1)-TS, and 112.1%, respectively.
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Affiliation(s)
- Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Jing Zhang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Xiao-Zhong Zhong
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Li Tan
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Kenji Kida
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1, First Ring Road, Chengdu, Sichuan 610065, China.
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93
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Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil. Appl Microbiol Biotechnol 2016; 100:6815-6826. [DOI: 10.1007/s00253-016-7502-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 12/16/2022]
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94
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Zhang J, Zhou X, Chen L, Chen Z, Chu J, Li Y. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes. World J Microbiol Biotechnol 2016; 32:85. [DOI: 10.1007/s11274-016-2042-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/29/2016] [Indexed: 11/24/2022]
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95
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Grunert O, Reheul D, Van Labeke MC, Perneel M, Hernandez-Sanabria E, Vlaeminck SE, Boon N. Growing media constituents determine the microbial nitrogen conversions in organic growing media for horticulture. Microb Biotechnol 2016; 9:389-99. [PMID: 27005434 PMCID: PMC4835575 DOI: 10.1111/1751-7915.12354] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 11/27/2022] Open
Abstract
Vegetables and fruits are an important part of a healthy food diet, however, the eco‐sustainability of the production of these can still be significantly improved. European farmers and consumers spend an estimated €15.5 billion per year on inorganic fertilizers and the production of N‐fertilizers results in a high carbon footprint. We investigated if fertilizer type and medium constituents determine microbial nitrogen conversions in organic growing media and can be used as a next step towards a more sustainable horticulture. We demonstrated that growing media constituents showed differences in urea hydrolysis, ammonia and nitrite oxidation and in carbon dioxide respiration rate. Interestingly, mixing of the growing media constituents resulted in a stimulation of the function of the microorganisms. The use of organic fertilizer resulted in an increase in amoA gene copy number by factor 100 compared to inorganic fertilizers. Our results support our hypothesis that the activity of the functional microbial community with respect to nitrogen turnover in an organic growing medium can be improved by selecting and mixing the appropriate growing media components with each other. These findings contribute to the understanding of the functional microbial community in growing media and its potential role towards a more responsible horticulture.
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Affiliation(s)
- Oliver Grunert
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium.,Peltracom, Skaldenstraat 7a, Desteldonk, 9042, Belgium
| | - Dirk Reheul
- Department of Plant Production, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | | | | | - Emma Hernandez-Sanabria
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Siegfried E Vlaeminck
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium.,Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium
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96
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Sauder LA, Ross AA, Neufeld JD. Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria. FEMS Microbiol Lett 2016; 363:fnw052. [PMID: 26946536 DOI: 10.1093/femsle/fnw052] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2016] [Indexed: 11/14/2022] Open
Abstract
Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested onNitrosopumilus maritimus, two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representative Nitrosomonas europaea All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway.
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Affiliation(s)
- Laura A Sauder
- Department of Biology, University of Waterloo, 200 University Ave. W. Waterloo, ON N2L 3G1, Canada
| | - Ashley A Ross
- Department of Biology, University of Waterloo, 200 University Ave. W. Waterloo, ON N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Ave. W. Waterloo, ON N2L 3G1, Canada
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97
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Wang HB, Han LR, Feng JT, Zhang X. Evaluation of microbially enhanced composting of sophora flavescens residues. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2016; 51:63-70. [PMID: 26578168 DOI: 10.1080/03601234.2015.1080503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The effects of inoculants on the composting of Sophora flavescens residues were evaluated based on several physical, chemical and biological parameters, as well as the infrared spectra. Compared to the control compost without inoculants, the treatment compost with inoculants (Bacillus subtilis strain G-13 and Chaetomium thermophilum strain GF-1) had a significantly longer thermophilic duration, higher cellulase activity and a higher degradation rate of cellulose, hemicellulose and lignin (P < 0.05). Thus, a higher maturity degree of compost with apparently lower C:N ratio (15.88 vs. 17.77) and NH4-N:NO3-N ratio (0.16 vs. 0.20) was obtained with the inoculation comparing with the control (P < 0.05). Besides, the inoculants could markedly accelerate the composting process and increase the maturity degree of compost as indicated by the germination index (GI) in which the treatment reached the highest GI of 133.2% at day 15 while the control achieved the highest GI of 125.7% at day 30 of the composting. Inoculation with B. subtilis and C. thermophilum is a useful method to enhance the S. flavescens residues composting according to this study.
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Affiliation(s)
- Hai B Wang
- a Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A & F University , Yangling , P. R. China
| | - Li R Han
- a Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A & F University , Yangling , P. R. China
| | - Jun T Feng
- a Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A & F University , Yangling , P. R. China
| | - Xing Zhang
- a Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A & F University , Yangling , P. R. China
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98
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Lu S, Liu X, Ma Z, Liu Q, Wu Z, Zeng X, Shi X, Gu Z. Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond. Front Microbiol 2016; 6:1539. [PMID: 26834709 PMCID: PMC4718984 DOI: 10.3389/fmicb.2015.01539] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 12/21/2015] [Indexed: 11/19/2022] Open
Abstract
Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster.
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Affiliation(s)
- Shimin Lu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery SciencesShanghai, China; College of Fisheries and Life, Shanghai Ocean UniversityShanghai, China
| | - Xingguo Liu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
| | - Zhuojun Ma
- Chinese Academy of Fishery Sciences Beijing, China
| | - Qigen Liu
- College of Fisheries and Life, Shanghai Ocean University Shanghai, China
| | - Zongfan Wu
- Tongren Municipal Agricultural Commission (Government, Public) Tongren, China
| | - Xianlei Zeng
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery SciencesShanghai, China; College of Fisheries and Life, Shanghai Ocean UniversityShanghai, China
| | - Xu Shi
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
| | - Zhaojun Gu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
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99
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Lima-Perim JE, Romagnoli EM, Dini-Andreote F, Durrer A, Dias ACF, Andreote FD. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest. PLoS One 2016; 11:e0146566. [PMID: 26752633 PMCID: PMC4713446 DOI: 10.1371/journal.pone.0146566] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/18/2015] [Indexed: 12/21/2022] Open
Abstract
The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.
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Affiliation(s)
| | | | - Francisco Dini-Andreote
- Microbial Ecology Group, Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Ademir Durrer
- Department of Soil Science, ESALQ/USP, University of São Paulo, Piracicaba, Brazil
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100
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Gan XH, Zhang FQ, Gu JD, Guo YD, Li ZQ, Zhang WQ, Xu XY, Zhou Y, Wen XY, Xie GG, Wang YF. Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China. Antonie van Leeuwenhoek 2015; 109:237-51. [DOI: 10.1007/s10482-015-0627-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/19/2015] [Indexed: 10/22/2022]
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