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Huang H, He M, Liu X, Ma X, Yang Y, Shen Y, Yang Y, Zhen Y, Wang J, Zhang Y, Wang S, Shan X, Fan W, Guo D, Niu Z. The dynamic features and microbial mechanism of nitrogen transformation for hydrothermal aqueous phase as fertilizer in dryland soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120643. [PMID: 38513582 DOI: 10.1016/j.jenvman.2024.120643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 02/19/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
Hydrothermal aqueous phase (HAP) contains abundant organics and nutrients, which have potential to partially replace chemical fertilizers for enhancing plant growth and soil quality. However, the underlying reasons for low available nitrogen (N) and high N loss in dryland soil remain unclear. A cultivation experiment was conducted using HAP or urea to supply 160 mg N kg-1 in dryland soil. The dynamic changes of soil organic matters (SOMs), pH, N forms, and N cycling genes were investigated. Results showed that SOMs from HAP stimulated urease activity and ureC, which enhanced ammonification in turn. The high-molecular-weight SOMs relatively increased during 5-30 d and then biodegraded during 30-90 d, which SUV254 changed from 0.51 to 1.47 to 0.29 L-1 m-1. This affected ureC that changed from 5.58 to 5.34 to 5.75 lg copies g-1. Relative to urea, addition HAP enhanced ON mineralization by 8.40 times during 30-90 d due to higher ureC. It decreased NO3-N by 65.35%-77.32% but increased AOB and AOA by 0.25 and 0.90 lg copies g-1 at 5 d and 90 d, respectively. It little affected nirK and increased nosZ by 0.41 lg copies g-1 at 90 d. It increased N loss by 4.59 times. The soil pH for HAP was higher than that for urea after 11 d. The comprehensive effects of high SOMs and pH, including ammonification enhancement and nitrification activity inhibition, were the primary causes of high N loss. The core idea for developing high-efficiency HAP fertilizer is to moderately inhibit ammonification and promote nitrification.
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Affiliation(s)
- Hua Huang
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China; Engineering Research Center of Efficient Exploitation of Oil and Gas Resources and Protection Ecological Environment, Yan'an, 716000, China; Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an, 716000, Shaanxi, China
| | - Maoyuan He
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Xiaoyan Liu
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Xiaoli Ma
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Ying Yang
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Yuanlei Shen
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Yujia Yang
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Yanzhong Zhen
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China; Engineering Research Center of Efficient Exploitation of Oil and Gas Resources and Protection Ecological Environment, Yan'an, 716000, China
| | - Jian Wang
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China; Engineering Research Center of Efficient Exploitation of Oil and Gas Resources and Protection Ecological Environment, Yan'an, 716000, China
| | - Yongtao Zhang
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China; Engineering Research Center of Efficient Exploitation of Oil and Gas Resources and Protection Ecological Environment, Yan'an, 716000, China
| | - Shuai Wang
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China; Engineering Research Center of Efficient Exploitation of Oil and Gas Resources and Protection Ecological Environment, Yan'an, 716000, China
| | - Xianying Shan
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Wenyan Fan
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Di Guo
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China; Engineering Research Center of Efficient Exploitation of Oil and Gas Resources and Protection Ecological Environment, Yan'an, 716000, China
| | - Zhirui Niu
- School of Petroleum Engineering and Environmental Engineering, Yan'an Key Laboratory of Agricultural Solid Waste Resource Utilization, Yan'an Key Laboratory of Environmental Monitoring and Remediation, Yan'an University, Yan'an, 716000, Shaanxi, China; Engineering Research Center of Efficient Exploitation of Oil and Gas Resources and Protection Ecological Environment, Yan'an, 716000, China; Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an, 716000, Shaanxi, China.
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Yang W, Cui H, Liu Q, Wang F, Liao H, Lu P, Qin S. Effect of nitrogen reduction by chemical fertilization with green manure (Vicia sativa L.) on soil microbial community, nitrogen metabolism and and yield of Uncaria rhynchophylla by metagenomics. Arch Microbiol 2024; 206:106. [PMID: 38363349 DOI: 10.1007/s00203-024-03839-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/24/2023] [Accepted: 01/06/2024] [Indexed: 02/17/2024]
Abstract
Uncaria rhynchophylla is an important herbal medicine, and the predominant issues affecting its cultivation include a single method of fertilizer application and inappropriate chemical fertilizer application. To reduce the use of inorganic nitrogen fertilization and increase the yield of Uncaria rhynchophylla, field experiments in 2020-2021 were conducted. The experimental treatments included the following categories: S1, no fertilization; S2, application of chemical NPK fertilizer; and S3-S6, application of chemical fertilizers and green manures, featuring nitrogen fertilizers reductions of 0%, 15%, 30%, and 45%, respectively. The results showed that a moderate application of nitrogen fertilizer when combined with green manure, can help alleviate soil acidification and increase urease activity. Specifically, the treatment with green manure provided in a 14.71-66.67% increase in urease activity compared to S2. Metagenomics sequencing results showed a decrease in diversity in S3, S4, S5, and S6 compared to S2, but the application of chemical fertilizer with green manure promoted an increase in the relative abundance of Acidobacteria and Chloroflexi. In addition, the nitrification pathway displayed a progressive augmentation in tandem with the reduction in nitrogen fertilizer and application of green manure, reaching its zenith at S5. Conversely, other nitrogen metabolism pathways showed a decline in correlation with diminishing nitrogen fertilizer dosages. The rest of the treatments showed an increase in yield in comparison to S1, S5 showing significant differences (p < 0.05). In summary, although S2 demonstrate the ability to enhance soil microbial diversity, it is important to consider the long-term ecological impacts, and S5 may be a better choice.
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Affiliation(s)
- Wansheng Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - HongHao Cui
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
- Institute of Soil Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Qian Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Fang Wang
- Guizhou Industry Polytechnic College, Guiyang, 550008, China
| | - Heng Liao
- Institute of Soil Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Ping Lu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | - Song Qin
- Institute of Soil Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
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Wei C, Su F, Yue H, Song F, Li H. Spatial distribution characteristics of denitrification functional genes and the environmental drivers in Liaohe estuary wetland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:1064-1078. [PMID: 38030842 DOI: 10.1007/s11356-023-30938-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
Genes nirS, nirK, and nosZ are specific for the denitrification process, which is associated with greenhouse gas N2O emission. The abundances and diversities of community containing these three genes are usually used as a common index to reflect the denitrification process, and they would be affected by differences in environmental factors caused by changes from warm to cold conditions. The quantification of denitrification in natural wetlands is complex, and straightforward identification of spatial distribution and drivers affecting the process is still developing. In this study, the bacterial communities, gene diversities, and relative abundances involved in denitrification were investigated in Liaohe Estuary Wetland. We analyzed the relative abundances, diversities, and communities of bacteria containing the three genes at warm and cold conditions using Illumina MiSeq sequencing and detected the potential environmental factors influencing their distribution by using a random forest algorithm. There are great differences in the community composition of the bacteria containing genes nirS, nirK, and nosZ. All the abundant taxa of nirS and nirK communities belonged to phylum Proteobacteria. Compared with the community composition of bacteria containing nirS and nirK, the community of bacteria containing nosZ is more diverse, and the subdivision taxa of phylum Euryarchaeota was also abundant in the community containing nosZ. The distribution characteristics of the relative abundance of nirS and nirK showed obvious differences both at warm and cold climate conditions. The oxidation-reduction potential, nitrite nitrogen, and salinity were detected as potential variables that might explain the diversity of nirS. The total nitrogen and nitrite nitrogen were the important variables for predicting the relative abundance of nirS at warm climate condition, while oxidation-reduction potential and pH contributed to the diversity of nirS at cold condition. The bulk density of sediment was detected as a potential variable affecting the relative abundance of nirK at warm and cold conditions, and diversity of nirK at warm condition, while nitrite nitrogen was detected as an important environmental factor for predicting the diversity of nirK at cold condition. Overall, our results show that the key environmental factors, which affect the relative abundance, diversity, and community of bacteria containing the functional denitrification genes, are not exactly the same, and the diversities of nirS, nirK, and nosZ have a higher environmental sensitivity than their relative abundances.
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Affiliation(s)
- Chao Wei
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China
| | - Fangli Su
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China.
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China.
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China.
| | - Hangyu Yue
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Fei Song
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China
| | - Haifu Li
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China
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Yang Y, Liu H, Zhang Y, Fang X, Zhong X, Lv J. Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments. Sci Rep 2023; 13:20722. [PMID: 38007550 PMCID: PMC10676402 DOI: 10.1038/s41598-023-44147-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/04/2023] [Indexed: 11/27/2023] Open
Abstract
The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3--N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.
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Affiliation(s)
- Yajun Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Hexiang Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Yang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Xianhui Fang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Xianbao Zhong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Jialong Lv
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China.
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Luo F, Liu W, Mi W, Ma X, Liu K, Ju Z, Li W. Legume-grass mixtures increase forage yield by improving soil quality in different ecological regions of the Qinghai-Tibet Plateau. FRONTIERS IN PLANT SCIENCE 2023; 14:1280771. [PMID: 37929174 PMCID: PMC10620939 DOI: 10.3389/fpls.2023.1280771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023]
Abstract
Introduction Information on the relationship between soil quality and forage yield of legume-grass mixtures in different ecological regions can guide decision-making to achieve eco-friendly and sustainable pasture production. This study's objective was to assess the effects of different cropping systems on soil physical properties, nitrogen fractions, enzyme activities, and forage yield and determine suitable legume-grass mixtures for different ecoregions. Methods Oats (Avena sativa L.), forage peas (Pisum sativum L.), common vetch (Vicia sativa L.), and fava beans (Vicia faba L.) were grown in monocultures and mixtures (YS: oats and forage peas; YJ: oats and common vetch; YC: oats and fava beans) in three ecological regions (HZ: Huangshui Valley; GN: Sanjiangyuan District; MY: Qilian Mountains Basin) in a split-plot design. Results The results showed that the forage yield decreased with increasing altitude, with an order of GN (3203 m a.s.l.; YH 8.89 t·ha-1) < HZ (2661 m; YH 9.38 t·ha-1) < MY (2513m; YH 9.78 t·ha-1). Meanwhile, the forage yield was higher for mixed crops than for single crops in all ecological regions. In the 0-10 cm soil layer, the contents of total nitrogen (TN), microbial biomass nitrogen (MBN), soil organic matter (SOM), soluble organic nitrogen (SON), urease (UE), nitrate reductase (NR), sucrase (SC), and bacterial community alpha diversity, as well as relative abundance of dominant bacteria, were higher for mixed crops than for oats unicast. In addition, soil physical properties, nitrogen fractions, and enzyme activities varied in a wider range in the 0-10 cm soil layer than in the 10-20 cm layer, with larger values in the surface layer than in the subsurface layer. MBN, SON, UE, SC and catalase (CAT) were significantly and positively correlated with forage yield (P < 0.05). Ammonium nitrogen (ANN), nitrate nitrogen (NN), SOM and cropping systems (R) were significantly and positively correlated with Shannon and bacterial community (P < 0.05). The highest yields in the three ecological regions were 13.00 t·ha-1 for YS in MY, 10.59 t·ha-1 for YC in GN, and 10.63 t·ha-1 for YS in HZ. Discussion We recommend planting oats and forage peas in the Qilian Mountains Basin, oats and fava beans in the Sanjiangyuan District, and oats and forage peas in Huangshui valley. Our results provide new insights into eco-friendly, sustainable, and cost-effective forage production in the Qinghai Alpine Region in China.
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Affiliation(s)
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
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Cui C, Shen J, Zhu Y, Chen X, Liu S, Yang J. Bioremediation of phenanthrene in saline-alkali soil by biochar- immobilized moderately halophilic bacteria combined with Suaeda salsa L. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163279. [PMID: 37019226 DOI: 10.1016/j.scitotenv.2023.163279] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 05/27/2023]
Abstract
Polycyclic aromatic hydrocarbon (PAH) contaminated saline-alkali soil is commonly salinized and hardened, which leads to low self-purification efficiency, making it difficult to reuse and remediate. In this study, pot experiments were conducted to investigate remediation of PAH contaminated saline-alkali soil using biochar-immobilized Martelella sp. AD-3, and Suaeda salsa L (S. salsa). Reduction in phenanthrene concentration, PAH degradation functional genes, and the microbial community in the soil were analyzed. The soil properties and plant growth parameters were also analyzed. After a 40-day remediation, the removal rate of phenanthrene by biochar-immobilized bacteria combined with S. salsa (MBP group) was 91.67 %. Additionally, soil pH and electrical conductivity (EC) reduced by 0.15 and 1.78 ds/m, respectively. The fresh weight and leaf pigment contents increased by 1.30 and 1.35 times, respectively, which effectively alleviated the growth pressure on S. salsa in PAH-contaminated saline-alkali soil. Furthermore, this remediation resulted in abundance of PAH degradation functional genes in the soil, with a value of 2.01 × 103 copies/g. The abundance of other PAH degraders such as Halomonas, Marinobacter, and Methylophaga in soil also increased. Furthermore, the highest abundance of Martelella genus was observed after the MBP treatment, indicating that strain AD-3 has a higher survival ability in the rhizosphere of S. salsa under the protection of biochar. This study provides a green, low-cost technique for remediation of PAH-contaminated saline-alkali soils.
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Affiliation(s)
- Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Jiamin Shen
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yi Zhu
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Shanghai Institute of Eco-Chongming, Fudan University, Shanghai 200438, China
| | - Xin Chen
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Siyuan Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jie Yang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; State Environment Protection Engineering Center for Urban Soil Contamination Control and Remediation, Shanghai Academy of Environmental Sciences, Shanghai 200233, China.
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Tahir M, Wei X, Liu H, Li J, Zhou J, Kang B, Jiang D, Yan Y. Mixed legume-grass seeding and nitrogen fertilizer input enhance forage yield and nutritional quality by improving the soil enzyme activities in Sichuan, China. FRONTIERS IN PLANT SCIENCE 2023; 14:1176150. [PMID: 37229108 PMCID: PMC10203570 DOI: 10.3389/fpls.2023.1176150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023]
Abstract
Information regarding relationships between forage yield and soil enzymes of legume-grass mixtures under nitrogen (N) fertilization can guide the decision-making during sustainable forage production. The objective was to evaluate the responses of forage yield, nutritional quality, soil nutrients, and soil enzyme activities of different cropping systems under various N inputs. Alfalfa (Medicago sativa L.), white clover (Trifolium repens L.), orchardgrass (Dactylis glomerata L.), and tall fescue (Festuca arundinacea Schreb.) were grown in monocultures and mixtures (A1: alfalfa, orchardgrass, and tall fescue; A2: alfalfa, white clover, orchardgrass, and tall fescue) under three N inputs (N1: 150 kg ha-1; N2, 300 kg ha-1; and N3: 450 kg ha-1) in a split plot arrangement. The results highlight that A1 mixture under N2 input had a greater forage yield of 13.88 t ha-1 year-1 than the other N inputs, whereas A2 mixture under N3 input had a greater forage of 14.39 t ha-1 year-1 than N1 input, but it was not substantially greater than N2 input (13.80 t ha-1 year-1). The crude protein (CP) content of grass monocultures and mixtures significantly (P < 0.05) increased with an increase in the rate of N input, and A1 and A2 mixtures under N3 input had a greater CP content of 18.91% and 18.94% dry matter, respectively, than those of grass monocultures under various N inputs. The A1 mixture under N2 and N3 inputs had a substantially greater (P < 0.05) ammonium N content of 16.01 and 16.75 mg kg-1, respectively, whereas A2 mixture under N3 had a greater nitrate N content of 4.20 mg kg-1 than the other cropping systems under various N inputs. The A1 and A2 mixtures under N2 input had a substantial higher (P < 0.05) urease enzyme activity of 0.39 and 0.39 mg g-1 24 h-1 and hydroxylamine oxidoreductase enzyme activity of 0.45 and 0.46 mg g-1 5 h-1, respectively, than the other cropping systems under various N inputs. Taken together, growing legume-grass mixtures under N2 input is cost-effective, sustainable, and eco-friendly, which provide greater forage yield and improved nutritional quality by the better utilization of resources.
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Affiliation(s)
- Muhammad Tahir
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Wei
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Haiping Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiayi Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiqiong Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bo Kang
- Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Dongmei Jiang
- Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Yanhong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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Cui H, Feng Y, Yin Z, Qu K, Wang L, Li J, Jin T, Bai Y, Cui Z. Organic carbon release, denitrification performance and microbial community of solid-phase denitrification reactors using the blends of agricultural wastes and artificial polymers for the treatment of mariculture wastewater. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 255:114791. [PMID: 36934547 DOI: 10.1016/j.ecoenv.2023.114791] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
This paper explored the possibility of heterotrophic denitrification driven by composite solid carbon sources in low carbon/nitrogen ratio marine recirculating aquaculture wastewater. In this study, two agricultural wastes, reed straw (RS), corn cob (CC) and two artificial polymers, polycaprolactone (PCL), poly3-hydroxybutyrate-hydroxypropionate (PHBV) were mixed in a 1:1 ratio to compare the carbon release characteristics of the four composite carbon sources (RS+PCL, RS+PHBV, CC+PCL, and CC+PHBV) and their effects on improving the mariculture wastewater for denitrification. Dissolved organic carbon (DOC) after carbon source release (4.96-1.07 mg/g), total organic carbon/chemical oxygen demand (1.9-0.79) and short-chain fatty acids (SCFAs) (4.23-0.21 mg/g) showed that all the four composite solid carbon sources had excellent organic carbon release ability, and the CC+PCL group had the highest release of DOC and SCFAs. Energy-dispersive X-ray spectroscopy, scanning electron microscopy, and Fourier-transform infrared spectroscopy were used to observe the changes in the surface characteristics of the composite carbon source before and after application. And results showed that the stable internal structure enabled CC+PCL group to have continuous carbon release performance and achieved the maximum denitrification efficiency (93.32 %). The NRE results were supported by the abundance of the Proteobacteria microbial community at the phylum level and Marinobacter at the genus level. Quantitative real-time PCR (q-PCR) indicated CC-containing composite carbon source groups have good nitrate reduction ability, while PCL-containing composite carbon source groups have better nitrite reduction level. In conclusion, the carbon source for agricultural wastes and artificial polymers can be used as an economic and effective solid carbon source for denitrification and treatment of marine recirculating aquaculture wastewater.
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Affiliation(s)
- Hongwu Cui
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laoshan Laboratory, Qingdao 266237, China
| | - Yuna Feng
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; National Experimental Teaching Demonstration Center for Aquatic Science, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Zhendong Yin
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Keming Qu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laoshan Laboratory, Qingdao 266237, China
| | - Lu Wang
- Laoshan Laboratory, Qingdao 266237, China
| | - Jiaxin Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Tongtong Jin
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Ying Bai
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laoshan Laboratory, Qingdao 266237, China
| | - Zhengguo Cui
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laoshan Laboratory, Qingdao 266237, China.
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9
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Feng Y, Wang L, Yin Z, Cui Z, Qu K, Wang D, Wang Z, Zhu S, Cui H. Comparative investigation on heterotrophic denitrification driven by different biodegradable polymers for nitrate removal in mariculture wastewater: Organic carbon release, denitrification performance, and microbial community. Front Microbiol 2023; 14:1141362. [PMID: 36891393 PMCID: PMC9986267 DOI: 10.3389/fmicb.2023.1141362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/31/2023] [Indexed: 02/22/2023] Open
Abstract
Heterotrophic denitrification is widely studied to purify freshwater wastewater, but its application to seawater wastewater is rarely reported. In this study, two types of agricultural wastes and two types of synthetic polymers were selected as solid carbon sources in denitrification process to explore their effects on the purification capacity of low-C/N marine recirculating aquaculture wastewater (NO3 --N 30 mg/L, salinity 32‰). The surface properties of reed straw (RS), corn cob (CC), polycaprolactone (PCL) and poly3-hydroxybutyrate-hydroxypropionate (PHBV) were evaluated by Brunauer-Emmett-Teller, Scanning electron microscope and Fourier-transform infrared spectroscopy. Short-chain fatty acids, dissolved organic carbon (DOC), and chemical oxygen demand (COD) equivalents were used to analyze the carbon release capacity. Results showed that agricultural waste had higher carbon release capacity than PCL and PHBV. The cumulative DOC and COD of agricultural waste were 0.56-12.65 and 1.15-18.75 mg/g, respectively, while those for synthetic polymers were 0.07-1.473 and 0.045-1.425 mg/g, respectively. The removal efficiency of nitrate nitrogen (NO3 --N) was CC 70.80%, PCL 53.64%, RS 42.51%, and PHBV 41.35%. Microbial community analysis showed that Proteobacteria and Firmicutes were the most abundant phyla in agricultural wastes and biodegradable natural or synthetic polymers. Quantitative real-time PCR indicated the conversion from nitrate to nitrogen was achieved in all four carbon source systems, and all six genes had the highest copy number in CC. The contents of medium nitrate reductase, nitrite reductase and nitrous oxide reductase genes in agricultural wastes were higher than those in synthetic polymers. In summary, CC is an ideal carbon source for denitrification technology to purify low C/N recirculating mariculture wastewater.
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Affiliation(s)
- Yuna Feng
- National Experimental Teaching Demonstration Center for Aquatic Science, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Lu Wang
- Marine Life Research Center, Laoshan Laboratory, Qingdao, China
| | - Zhendong Yin
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Zhengguo Cui
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Marine Life Research Center, Laoshan Laboratory, Qingdao, China
| | - Keming Qu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Marine Life Research Center, Laoshan Laboratory, Qingdao, China
| | - Dawei Wang
- National Experimental Teaching Demonstration Center for Aquatic Science, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Zhanying Wang
- National Experimental Teaching Demonstration Center for Aquatic Science, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Shengmin Zhu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Hongwu Cui
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Marine Life Research Center, Laoshan Laboratory, Qingdao, China
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10
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The Contribution of Nitrate Dissimilation to Nitrate Consumption in narG- and napA-Containing Nitrate Reducers with Various Oxygen and Nitrate Supplies. Microbiol Spectr 2022; 10:e0069522. [PMID: 36453888 PMCID: PMC9769761 DOI: 10.1128/spectrum.00695-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Nitrate reducers containing narG or napA play an important role in the nitrogen cycle, but little is known about their functional differentiations in relation to environmental changes. In this study, three types of nitrate reducers in the genus Pseudomonas, including strains containing narG (G type), napA (A type) and both narG and napA (GA type), were selected to explore their functional performances under varied nitrate and oxygen concentrations. Their growth characteristics, nitrate consumption, and dissimilatory nitrate-reducing activity were investigated. Growth and nitrate consumption of all three types of strains were generally promoted with increasing oxygen and nitrate concentrations. However, their dissimilatory nitrate-reducing activities were restricted by oxygen supply. When supplied with 0.25 mM KNO3, A-type strains showed a higher growth rate but lower activity of dissimilatory nitrate reduction (DNR) than G-type strains, regardless of oxygen concentration. However, when nitrate concentration increased to 0.75 mM or 5 mM, G-type strains displayed stronger capability of nitrate consumption and DNR than A-type strains under anaerobic conditions, whereas under oxygenated conditions, A-type strains exhibited higher growth and nitrate consumption but weaker DNR than G-type strains. The GA-type strains appeared similar to G type under anaerobic conditions but performed more similarly to A type in aerobic environments. In summary, the nitrate consumption of narG-containing nitrate reducers is mainly caused by DNR in both anaerobic and aerobic environments, while the large proportion of nitrate consumption in A-type nitrate reducers under the aerobic condition is attributed to the assimilation by cell growth. IMPORTANCE Nitrate reducers containing narG or napA are ubiquitous, but little is known about their functional performance in various environments. Our study provides an important clue that the nitrate consumption of narG-containing strains is mainly caused by dissimilatory reduction in the environments, while that of napA-containing nitrate reducers under anaerobic conditions is ascribed to nitrate dissimilation but under the aerobic condition is attributed to the assimilation by cell growth. This finding broadens the understanding of aerobic nitrate reduction in the nitrogen cycle and highlights the important role of narG-containing bacteria in nitrate reduction under aerobic conditions.
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11
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Mehmood MA, Fu Y, Zhao H, Cheng J, Xie J, Jiang D. Enrichment of bacteria involved in the nitrogen cycle and plant growth promotion in soil by sclerotia of rice sheath blight fungus. STRESS BIOLOGY 2022; 2:32. [PMID: 37676387 PMCID: PMC10441917 DOI: 10.1007/s44154-022-00049-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/27/2022] [Indexed: 09/08/2023]
Abstract
Rice sheath blight pathogen, Rhizoctonia solani, produces numerous sclerotia to overwinter. As a rich source of nutrients in the soil, sclerotia may lead to the change of soil microbiota. For this purpose, we amended the sclerotia of R. solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points. At the phyla level, Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control. An increased abundance of ammonia-oxidizing bacterium (AOB) Nitrosospira and Nitrite oxidizing bacteria (NOB) i.e., Nitrospira was observed, where the latter is reportedly involved in the nitrifier denitrification. Moreover, Thiobacillus, Gemmatimonas, Anaeromyxobacter and Geobacter, the vital players in denitrification, N2O reduction and reductive nitrogen transformation, respectively, depicted enhanced abundance in R. solani sclerotia-amended samples. Furthermore, asymbiotic nitrogen-fixing bacteria, notably, Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control. Plant growth promoting bacteria, such as Kribbella, Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil. As per our knowledge, this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R. solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.
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Affiliation(s)
- Mirza Abid Mehmood
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
- Plant Pathology, Institute of Plant Protection, MNS University of Agriculture, Multan, 60000, Pakistan
| | - Yanping Fu
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
| | - Huizhang Zhao
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China.
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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12
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Yang Y, Liu H, Lv J. Response of N 2O emission and denitrification genes to different inorganic and organic amendments. Sci Rep 2022; 12:3940. [PMID: 35273224 PMCID: PMC8913736 DOI: 10.1038/s41598-022-07753-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/09/2022] [Indexed: 11/10/2022] Open
Abstract
Denitrification is a key biochemical process in nitrogen cycling and nitrous oxide (N2O) production. In this study, the impacts of different inorganic and organic amendments (OAs) on the abundance of denitrifying genes (nirS, nirK and nosZ) and the level of N2O emission were examined with incubation experiments. Six treatments included the indicated applications: (i) no fertilization (CK); (ii) urea application alone (U); (iii) wheat straw plus urea (U + WS); (iv) pig manure plus urea (U + PM); (v) compost product plus urea (U + CP); and (vi) improved compost product plus urea (U + IC). The results indicated that all fertilization treatments increased accumulative N2O emissions compared with the CK treatment. The U + WS, U + PM and U + CP treatments increased N2O emissions by 2.12–141.3%, and the U + IC treatment decreased N2O emissions by 23.24% relative to the U treatment. nirK was the dominant denitrification gene rather than nirS and nosZ found in soil. Additionally, the highest abundance of nirK gene was that with the U + PM treatment, and the lowest was that with the U + IC treatment. Additionally, changes in the nirK gene were highly correlated with levels of dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and nitrate nitrogen (NO3–N). Automatic linear modeling revealed that N2O emission was closely related to the nirK gene, DOC and NO3–N. Overall, the use of urea and improved compost as co-amendments retarded N2O emission to a considerable degree compared with other OA additions.
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Affiliation(s)
- Yajun Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, People's Republic of China
| | - Hexiang Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, People's Republic of China
| | - Jialong Lv
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China. .,Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, People's Republic of China.
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13
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Effects of Plastic versus Straw Mulching Systems on Soil Microbial Community Structure and Enzymes in Strawberry Cultivation. SOIL SYSTEMS 2022. [DOI: 10.3390/soilsystems6010021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This study aimed to evaluate changes in abundance, structure, and enzyme activity of the soil microbiome in response to 4 years of mulching using either black polyethylene plastic film (PM) or wheat straw (SM). Soil samples (depth 0–5 and 5–10 cm) were collected from conventional strawberry plots, in two samplings: 1 week prior (S1) and 7 weeks after straw application (S2). Selected soil properties were monitored in each system and the abundance and structure of microbial communities were characterized via phospholipid fatty acid (PLFA) analysis. The investigation of soil microbial functions included activities of the enzymes chitinase, leucine aminopeptidase, and acid phosphatase, as well as function genes involved in nitrogen transformation. Each mulch system resulted in distinct physicochemical properties. In particular, a pH value higher by one-unit under PM (7.6 ± 0.3) compared to SM (6.5 ± 0.3) was observed. Values for SOC, DOC, and total-N were 15%, 22%, and 16% higher in PM than in SM. The microbial biomass (total PLFAs) was 1.5-fold higher in SM compared to PM. The abundance of soil fungi (F) and bacteria (B) increased by 37% and 44% after straw incorporation compared to PM (S2). In particular, Gram-negative bacteria (gr–) increased by twofold in SM. Consequently, wider F:B and gr+:gr– ratios were observed in PM. According to the shifts in microbial abundance, the activity of the enzyme chitinase was lower by 27% in PM, while the activity of the acid phosphatase increased by 32%. Denitrification genes were not affected by the mulching systems. In conclusion, the abundance and structure of the investigated microbial groups and the enzyme activities were strongly influenced by the mulching system. In detail, effects on microbiota were primarily attributed to the altered soil pH and probably the input of degradable organic matter with straw mulching in SM. This resulted in higher abundance of soil microorganisms in SM, although measures within this cultivation system such as fungicide application may have exerted adverse effects on the microbiota.
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14
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Chen Q, Yuan Y, Hu Y, Wang J, Si G, Xu R, Zhou J, Xi C, Hu A, Zhang G. Excessive nitrogen addition accelerates N assimilation and P utilization by enhancing organic carbon decomposition in a Tibetan alpine steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142848. [PMID: 33268263 DOI: 10.1016/j.scitotenv.2020.142848] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 09/23/2020] [Accepted: 10/03/2020] [Indexed: 05/23/2023]
Abstract
High amounts of deposited nitrogen (N) dramatically influence the stability and functions of alpine ecosystems by changing soil microbial community functions, but the mechanism is still unclear. To investigate the impacts of increased N deposition on microbial community functions, a 2-year multilevel N addition (0, 10, 20, 40, 80 and 160 kg N ha-1 year-1) field experiment was set up in an alpine steppe on the Tibetan Plateau. Soil microbial functional genes (GeoChip 4.6), together with soil enzyme activity, soil organic compounds and environmental variables, were used to explore the response of microbial community functions to N additions. The results showed that the N addition rate of 40 kg N ha-1 year-1 was the critical value for soil microbial functional genes in this alpine steppe. A small amount of added N (≤40 kg N ha-1 year-1) had no significant effects on the abundance of microbial functional genes, while high amounts of added N (>40 kg N ha-1 year-1) significantly increased the abundance of soil organic carbon degradation genes. Additionally, the abundance of microbial functional genes associated with NH4+, including ammonification, N fixation and assimilatory nitrate reduction pathways, was significantly increased under high N additions. Further, high N additions also increased soil organic phosphorus utilization, which was indicated by the increase in the abundance of phytase genes and alkaline phosphatase activity. Plant richness, soil NO2-/NH4+ and WSOC/WSON were significantly correlated with the abundance of microbial functional genes, which drove the changes in microbial community functions under N additions. These findings help us to predict that increased N deposition in the future may alter soil microbial functional structure, which will lead to changes in microbially-mediated biogeochemical dynamics in alpine steppes on the Tibetan Plateau and will have extraordinary impacts on microbial C, N and P cycles.
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Affiliation(s)
- Qiuyu Chen
- CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yanli Yuan
- CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yilun Hu
- CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Wang
- Land and Resources College, China West Normal University, Nanchong 637009, Sichuan, China
| | - Guicai Si
- Lanzhou Center for Oil and Gas Resources, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Ri Xu
- CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University Oklahoma, Norman, OK 73019, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ang Hu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Gengxin Zhang
- CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China.
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15
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Chen J, Zhang Y, Yang Y, Tao T, Sun X, Guo P. Effects of increasing organic nitrogen inputs on CO 2, CH 4, and N 2O fluxes in a temperate grassland. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115822. [PMID: 33130444 DOI: 10.1016/j.envpol.2020.115822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 10/08/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Understanding future climate change requires accurate estimates of the impacts of atmospheric nitrogen (N) deposition, composed of both inorganic and organic compounds, on greenhouse gas (GHG) fluxes in grassland ecosystems. However, previous studies have focused on inorganic compounds and have not considered the potential effects of organic N sources. Here, we conducted a grassland experiment that included organic, inorganic N, and a mix of them at a ratio of 4:6, with two input rates, to study N inputs induced CO2, CH4, and N2O fluxes, as well as the potential abiotic and biotic mechanisms driving the fluxes. We found that N compositions significantly affected fluxes each of the three GHGs. Greater organic N decreased the impacts of N addition on CO2 and N2O emissions, caused primarily by low rates of increase in substrates (soil available N) for production of CO2 and N2O resulting from high ammonia volatilization rather than changes in microbial activity. Also, greater organic N slightly stimulated CH4 uptake. Nitrogen composition effects on CO2 emissions and CH4 uptake were independent of N input rates and measurement dates, but N2O emissions showed stronger responses to inorganic N under high N addition and in June. These results suggest that future studies should consider the source of N to improve our prediction of future climate impact of N deposition, and that management of N fertilization can help mitigate GHG emissions.
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Affiliation(s)
- Jihui Chen
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China; College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Yingjun Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China; College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yi Yang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; Department of Environmental Studies, Dartmouth College, Hanover, NH, 03755, USA
| | - Tingting Tao
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao Sun
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Peng Guo
- School of Biological Science and Engineering, Hebei University of Science and Technology, Yuxiang Street 26, Shijiazhuang, 050018, China
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16
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Chen Q, Fan J, Ming H, Su J, Wang Y, Wang B. Effects of environmental factors on denitrifying bacteria and functional genes in sediments of Bohai Sea, China. MARINE POLLUTION BULLETIN 2020; 160:111621. [PMID: 32919123 DOI: 10.1016/j.marpolbul.2020.111621] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
The ability of denitrifying microorganisms to respond to different ecological pressures remains unknown, especially in marine sediments rich in various heavy metals. Here, gene abundance and transcriptional abundance of five functional denitrification genes (narG, nirK, nirS, norB, and nosZ) in Bohai Sea sediments were examined, and high-throughput Illumina sequencing was used to analyze the community structure of nirK and nirS denitrifying bacteria. The nirS- and nirK-type denitrifying bacteria were classified into different genera. The heavy metal content in sediments was negatively correlated with transcriptional abundance of denitrifying genes, and RNA: DNA ratio for each gene was highest in central Bohai Sea. These results indicated the distribution of nitrite reductase denitrifying bacterial communities was affected by depth, total nitrogen, total phosphorus and sediment grain size. Heavy metal contamination in sediment environment may negatively regulate the transcriptional abundance of denitrifying genes and cause geographical differences in the denitrifying bacterial community structure.
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Affiliation(s)
- Quanrui Chen
- National Marine Environmental Monitoring Center, Dalian 116023, China; Xiamen University, Xiamen 361000, China
| | - Jingfeng Fan
- National Marine Environmental Monitoring Center, Dalian 116023, China.
| | - Hongxia Ming
- National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jie Su
- National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Yantao Wang
- National Marine Environmental Monitoring Center, Dalian 116023, China; Dalian Ocean University, Dalian 116000, China
| | - Bin Wang
- Dalian Ocean University, Dalian 116000, China
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17
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Li J, Wang G, Yan B, Liu G. The responses of soil nitrogen transformation to nitrogen addition are mainly related to the changes in functional gene relative abundance in artificial Pinus tabulaeformis forests. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 723:137679. [PMID: 32213396 DOI: 10.1016/j.scitotenv.2020.137679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/23/2020] [Accepted: 03/01/2020] [Indexed: 06/10/2023]
Abstract
The increase of soil nitrogen (N) availability may alter soil microbial community composition and the natural N cycle in forest ecosystems. However, the responses of soil microbial nitrogen functional genes (NFGs) to N addition and their consequent effect on the N-cycle processes are poorly understood. In this study, soil samples were collected from an artificial Pinus tabulaeformis forest located in Loess Plateau (China) to which N at four different concentrations was added (0 [N0], 3 [N3], 6 [N6], and 9 [N9] g N m-2 y-1) for 4 years. We quantified the relative abundance of NFGs using functional gene microarray GeoChip 5.0 and determined net N transformation and N2O emission rates in a 14-day incubation experiment. The results showed that N3 and N6 treatments did not significantly affect the total relative abundance and diversity of NFGs assemblage but significantly increased the relative abundance of specific genes for the NH3 cycle (ureC, nirA, and nrfA), and nitrification (amoA) and denitrification (norB). These positive effects were related to the increase in soil organic C, NO3--N, and microbial biomass C (MBC). N9 treatment significantly decreased the relative abundance of all NFGs, and this negative impact was correlated with reduced dissolved organic C and MBC. Moreover, N addition significantly changed net N nitrification, mineralization, and N2O emission rates, and NFGs explained the higher variances in the N transformation processes than soil properties. Specifically, ammonia-oxidizing archaea (amoA-AOB) and MBC were the key factors related to net N nitrification; ureC, nirK, and MBC were the key factors related to net N mineralization; and narG and nirS were the key factors related to N2O emission. Our results show that global N deposition may mainly influence N transformation processes by regulating the corresponding NFG relative abundance, thereby affecting the N cycle in forest soils.
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Affiliation(s)
- Jingjing Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, Shaanxi Province, China
| | - Guoliang Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, Shaanxi Province, China; Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Yangling 712100, Shaanxi, China.
| | - Benshuai Yan
- Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Yangling 712100, Shaanxi, China
| | - Guobin Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, Shaanxi Province, China; Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Yangling 712100, Shaanxi, China.
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Li Z, Wang L, Wu J, Xu Y, Wang F, Tang X, Xu J, Ok YS, Meng J, Liu X. Zeolite-supported nanoscale zero-valent iron for immobilization of cadmium, lead, and arsenic in farmland soils: Encapsulation mechanisms and indigenous microbial responses. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:114098. [PMID: 32041084 DOI: 10.1016/j.envpol.2020.114098] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/22/2020] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
Zeolite-supported nanoscale zero-valent iron (Z-NZVI) has great potential for metal(loid) removal, but its encapsulation mechanisms and ecological risks in real soil systems are not completely clear. We conducted long-term incubation experiments to gain new insights into the interactions between metal(loid)s (Cd, Pb, As) and Z-NZVI in naturally contaminated farmland soils, as well as the alteration of indigenous bacterial communities during soil remediation. With the pH-adjusting and adsorption capacities, 30 g kg-1 Z-NZVI amendment significantly decreased the available metal(loid) concentrations by 10.2-96.8% and transformed them into strongly-bound fractions in acidic and alkaline soils after 180 d. An innovative magnetic separation of Z-NZVI from soils followed by XRD and XPS characterizations revealed that B-type ternary complexation, heterogeneous coprecipitation, and/or concurrent redox reactions of metal(loid)s, especially the formation of Cd3(AsO4)2, PbFe2(AsO4)2(OH)2, and As0, occurred only under specific soil conditions. Sequencing of 16S rDNA using Illumina MiSeq platform indicated that temporary shifts in iron-resistant/sensitive, pH-sensitive, denitrifying, and metal-resistant bacteria after Z-NZVI addition were ultimately eliminated because soil characteristics drove the re-establishment of indigenous bacterial community. Meanwhile, Z-NZVI recovered the basic activities of bacterial DNA replication and denitrification functions in soils. These results confirm that Z-NZVI is promising for the long-term remediation of metal(loid)s contaminated farmland soil without significant ecotoxicity.
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Affiliation(s)
- Zhangtao Li
- College of Environmental & Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Lu Wang
- College of Environmental & Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Jizi Wu
- College of Environmental & Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Yan Xu
- College of Environmental & Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Fan Wang
- College of Life & Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Xianjin Tang
- College of Environmental & Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Jianming Xu
- College of Environmental & Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Yong Sik Ok
- Korea Biochar Research Center & Division of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jun Meng
- School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, 310023, China
| | - Xingmei Liu
- College of Environmental & Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
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19
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Cao L, Yu X, Liu C, Liu M, Chen J, Qin H, Liang C, Xu Q, Penttinen P. Alteration of soil nitrifiers and denitrifiers and their driving factors during intensive management of Moso bamboo (Phyllostachys pubescens). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135236. [PMID: 31841899 DOI: 10.1016/j.scitotenv.2019.135236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
Abstract
Long-term intensive management, such as inorganic fertilization and soil tillage, have been reported to decrease soil organic carbon content (SOC) and diversity of soil bacterial communities, as well as increase N2O emissions in moso bamboo forests. However, the response of the N-cycling soil microbial community to intensive management remains unclear. To address this, we examined the effects of intensive moso bamboo management on nitrifying and denitrifying microorganisms. Soils receiving non-management (NM) and 10, 15, 20, and 25 years of intensive management (IM10, IM15, IM20, IM25) were characterized using quantitative real-time PCR (qPCR) and high-through sequencing methods. Our results showed that abundances of ammonia monooxygenase (amoA) from ammonia-oxidizing archaea (AOA) significantly increased (P < 0.05) and were greatest in IM15 (8.37 × 107 copies/g dry soils) and IM25 (5.42 × 107 copies/g dry soils) in top- and subsoils, respectively, while nitrous oxide reductase (nosZ) abundance significantly decreased by 59.1% (topsoil) and 36.4% (subsoil) in IM20 (P < 0.05). GroupI.1a-associated affiliating to AOA, and Bradyrhizobium affiliating to nosZ, were keys groups for nitrifiers and denitrifiers, respectively, and showed the greatest variations in response to long-term intensive management. Abundances of ammonia-oxidizing bacteria (AOB) and the nitrite reductase gene nirS were less affected, as were the dominant Nitrosospira species belonging to the AOB community. Except the AOB amoA abundance, soil nitrogen was found to be the main factor influencing the abundance, diversity, and composition of nitrifying genes, while denitrifying genes were mainly affected by SOC and available potassium, indicating that different factors control populations of nitrifiers and denitrifiers. Collectively, our study revealed that groupings of nitrifying and denitrifying microorganisms responded differently to intensive management. This information is of potential value towards identifying strategies to minimize nitrogen loss in moso bamboo plantations.
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Affiliation(s)
- Linhua Cao
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Xiao Yu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Caixia Liu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Ming Liu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Junhui Chen
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Hua Qin
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Chenfei Liang
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Qiufang Xu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
| | - Petri Penttinen
- College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
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20
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Avşar C, Aras ES. Quantification of denitrifier genes population size and its relationship with environmental factors. Arch Microbiol 2020; 202:1181-1192. [PMID: 32076734 DOI: 10.1007/s00203-020-01826-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The objectives of this study were to use real-time PCR for culture-independent quantification of the copy numbers of 16S rRNA and denitrification functional genes, and also the relationships between gene copy numbers and soil physicochemical properties. In this study, qPCR analysis of the soil samples showed 16S rRNA, nirS, nirK, nosZI and nosZII average densities of 3.0 × 108, 2.25 × 107, 2.9 × 105, 4.0 × 106 and 1.75 × 107 copies per gram of dry soil, respectively. In addition, the abundances of (nirS + nirK), nosZI and nosZII relative to 16S rRNA genes were 1.4-34.1%, 0.06-3.95% and 1.3-39%, respectively, confirming the low proportion of denitrifiers to total bacteria in soil. This showed that the non-denitrifying nosZII-type bacteria may contribute significantly to N2O consumption in the soil. Furthermore, the shifts in abundance and diversity of the total bacteria and denitrification functional gene copy numbers correlated significantly with the various soil factors. It is the first study in Turkey about the population size of denitrification functional genes in different soil samples. It also aims to draw attention to nitrous oxide-associated global warming.
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Affiliation(s)
- Cumhur Avşar
- Department of Biology, Faculty of Arts and Sciences, Sinop University, Sinop, Turkey.
| | - E Sümer Aras
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey
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21
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Chen D, Li Y, Wang C, Liu X, Wang Y, Shen J, Qin J, Wu J. Dynamics and underlying mechanisms of N 2O and NO emissions in response to a transient land-use conversion of Masson pine forest to tea field. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133549. [PMID: 31374503 DOI: 10.1016/j.scitotenv.2019.07.355] [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: 05/28/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Nowadays, there has been a rapid expansion of tea field converted from forestry for pursuing higher economic benefits. However, few researches focus on the effects of transient land-use conversion from Masson pine forest to artificial tea fields on soil N2O and NO emissions and the underlying mechanisms. A parallel field experiment was conducted from Masson pine forest and a newly converted tea plantation from Masson pine forest from 2013 to 2017 in subtropical central China. Masson pine forest conversion to tea field dramatically increased soil N2O and NO emissions (up to 4.00 ± 0.43 and 1.93 ± 0.45 kg N ha-1 yr-1, respectively) in the first year possibly due to enhanced soil organic N mineralization. With the extension of tea planting age, N2O and NO emissions showed an upward trend (ranged from 1.19 to 5.28, and 0.15 to 1.78 kg N ha-1 yr-1, respectively) influenced by fertilization and soil organic matter accumulation. The direct emission factors for N2O and NO in the newly converted tea fields were the largest in the first year (2.64 and 1.07%, respectively) after land-use conversion, and higher than the default value recommended by IPCC. The NO/N2O ratio was mainly lower than 1 in the fertilized tea field, and soil N2O and NO emission peaks mainly occurred in tea-growing season (wet season) with higher soil moisture and NH4+-N concentrations, and dominated by amoA-containing bacteria (AOB), suggesting nitrifier-denitrification could be the dominant process involved in soil nitrogenous gases emissions in tea field. These results can be summarized as dramatically increased soil N2O and NO emissions during the transient land-use conversion from Masson pine forest to tea field were possibly due to the substantial net soil organic N mineralization and the enhanced abundance of nitrification functional genes (AOB).
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Affiliation(s)
- Dan Chen
- Changsha Research Station for Agricultural & Environmental Monitoring and Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, China; Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Nanning 530001, China; School of Environmental and Chemical Engineering, Zhaoqing University, Zhaoqing 526061, China
| | - Yong Li
- Changsha Research Station for Agricultural & Environmental Monitoring and Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, China.
| | - Cong Wang
- College of Forestry, Guangxi University, Nanning 530004, China.
| | - Xinliang Liu
- Changsha Research Station for Agricultural & Environmental Monitoring and Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, China
| | - Yi Wang
- Changsha Research Station for Agricultural & Environmental Monitoring and Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, China
| | - Jianlin Shen
- Changsha Research Station for Agricultural & Environmental Monitoring and Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, China
| | - Jianqiao Qin
- School of Environmental and Chemical Engineering, Zhaoqing University, Zhaoqing 526061, China
| | - Jinshui Wu
- Changsha Research Station for Agricultural & Environmental Monitoring and Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, China
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Bai Y, Huang X, Zhou X, Xiang Q, Zhao K, Yu X, Chen Q, Jiang H, Nyima T, Gao X, Gu Y. Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China. PeerJ 2019; 7:e7356. [PMID: 31428538 PMCID: PMC6698129 DOI: 10.7717/peerj.7356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 06/26/2019] [Indexed: 11/20/2022] Open
Abstract
Background The Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier’s retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years). Methods The diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR). Results nosZ-denitrifiers were more abundant and diverse in soils from successional years 20–60 compared to 0–5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40–60 years) than in younger soils (≤20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0–20 years) and in the mature phase (40–60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the community composition of nosZ-denitrifiers (P < 0.05 by Monte Carlo permutation test within RDA analysis).
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Affiliation(s)
- Yan Bai
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiying Huang
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiangrui Zhou
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Quanju Xiang
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ke Zhao
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiumei Yu
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiang Chen
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hao Jiang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Tashi Nyima
- Institute of Agricultural Resources and Environmental Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Xue Gao
- Institute of Agricultural Resources and Environmental Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Yunfu Gu
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
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23
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Zhou B, Duan J, Xue L, Zhang J, Yang L. Effect of plant-based carbon source supplements on denitrification of synthetic wastewater: focus on the microbiology. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:24683-24694. [PMID: 31240662 DOI: 10.1007/s11356-019-05454-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
The effects of plant-based carbon source addition on wastewater NO3--N removal and the involved microorganisms, especially denitrifying bacteria, were investigated. A synthetic wastewater (NO3--N, 15 mg/L) was treated through the batch experiment, which included three inoculation cycles (7 days/cycle), and was conducted at 25 °C. Four natural plant substrates, namely, rice straw (RS), wheat straw (WS), ryegrass (RG), and reed (RD), were used as carbon sources and supplemented at the rate of 1% (w/v). The results showed that both RS and WS performed well in promoting NO3--N removal (79.55-97.07%). While RG removed only 22.08% of NO3--N in the first cycle, the removal efficiency increased afterward (86.09-95.82%). Conversely, the NO3--N removal rate of RD decreased from 95.10 to 24.77% as a result of its low ability to supply carbon. With respect to the microorganisms, the RS treatment resulted in more bacteria and denitrifying genes such as narG, nirK, nirS, and norB than other treatments, while the highest number of nosZ gene copies was recorded in the WS treatment. Sequencing results revealed that Firmicutes (18.19-56.96%), Proteobacteria (38.82-74.80%), and Bacteroidetes (3.15-4.15%) were three dominant bacterial phyla for RS, WS, and RD treatments. Furthermore, the genera Enterobacter, Massilia, and Bacillus were the main denitrifying bacteria participating in the NO3--N removal. Furthermore, correlation analysis indicated that the denitrifying genus Sphingobacterium played an important role in enhancing nitrogen removal. This study suggested that RS is the superior plant-based carbon source for denitrifying bioreactors used in agricultural runoff treatment.
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Affiliation(s)
- Beibei Zhou
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jingjing Duan
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Lihong Xue
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Linzhang Yang
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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24
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Ma Y, Zilles JL, Kent AD. An evaluation of primers for detecting denitrifiers via their functional genes. Environ Microbiol 2019; 21:1196-1210. [PMID: 30724437 DOI: 10.1111/1462-2920.14555] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 12/11/2022]
Abstract
Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.
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Affiliation(s)
- Yanjun Ma
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julie L Zilles
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Angela D Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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25
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Remarkable N 2O emissions by draining fallow paddy soil and close link to the ammonium-oxidizing archaea communities. Sci Rep 2019; 9:2550. [PMID: 30796347 PMCID: PMC6384938 DOI: 10.1038/s41598-019-39465-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/23/2019] [Indexed: 11/08/2022] Open
Abstract
Fallow paddies experience natural flooding and draining water status due to rainfall and evaporation, which could induce considerable nitrous oxide (N2O) emissions and need to be studied specially. In this study, intact soil columns were collected from a fallow paddy field and the flooding-draining process was simulated in a microcosm experiment. The results showed that both N2O concentrations in the soil and N2O emission rates were negligible during flooding period, which were greatly elevated by draining the fallow paddy soil. The remarkable N2O concentrations in the soil and N2O emission/h during draining both had significant relationships with the Arch-amoA gene (P < 0.01) but not the Bac-amoA, narG, nirK, nirS, and nosZ genes, indicating that the ammonium-oxidizing archaea (AOA) might be the important players in soil N2O net production and emissions after draining. Moreover, we observed that N2O concentrations in the upper soil layers (0-10 cm) were not significantly different from that in the 10-20 cm layer under draining condition (P > 0.05). However, the number of AOA and the nitrification substrate (NH4+-N) in the 0-10 cm layer were significantly higher than in the 10-20 cm layer (P < 0.01), indicating N2O production in the 0-10 cm layer might be higher than the measured concentration and would contribute considerably to N2O emissions as shorter distance of gas diffusion to the soil surface.
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26
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Restoration of Long-Term Monoculture Degraded Tea Orchard by Green and Goat Manures Applications System. SUSTAINABILITY 2019. [DOI: 10.3390/su11041011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Tea is an economic shrubby plant in tropical and subtropical regions of the world. To obtain high yield in tea cultivation, chemical fertilizer application rates have generally been used. However, a large quantity of chemical fertilizer application in a long-term continuously ratooned and monoculture tea orchard can inevitably lead to soil acidification and a decline in fertility. Therefore, the restoration of soil fertility and the sustainable development of tea planting by organic ways are critical for the tea industry. In this study, field trials were conducted in the tea orchard that was continuously ratooned and mono-cultured for 20 years. Nitrogen fertilizer (NF), Laredo soybeans green manure (LF), and goat manure (GM) treatments were applied to restore optimum acidity, soil fertility, microbial activity, and the community structure of a long-term continuously monoculture tea orchard. This paper investigated that the pH value was increased from 4.23 to 4.32 in GM and LF, respectively. Similarly, the content of exchangeable acidity (EA) was decreased by 1.21 and 1.46 cmol·kg−1 in GM and LF, respectively. Available nutrient results indicated that the content of NH4+-N was increased by 3.96, 4.38, NO3−-N by 1.07, 2.16, AP by 3.46, 6.86, AK by 0.26, 0.3 mg kg−1 in GM and LF treatments, respectively. Enzyme analysis revealed that the activity of urease and sucrase was promoted by 7.98 mg·g−1·24 h−1 and 6.77 mg·g−1·24 h−1, respectively, in LF treatment. Likewise, the activity of acid phosphatase and polyphenol oxidase was sharply increased by 2.3 mg·g−1 h−1 and 63.07 mg·g−1 h−1 in LF treatments. Additionally, the activity of urease, sucrase, acidic phosphatase, polyphenol oxidase, and peroxidase were also significantly increased by applying GM treatments. Meanwhile, LF and GM treatments significantly improved soil microbial biomass as well as low weight organic acid content in degraded tea rhizosphere. Furthermore, high throughput sequence results illustrated that the relative abundance of Rhizobiaceae and Bradyrhizobiaceae families increased in LF and GM treatments, respectively, which are mostly a kind of nitrogen fixer and plant growth promoting bacteria. Taken together, the physiological traits of the new sprouts and the biochemical components of new tea leaves were also significantly improved by GM and LF treatments. From this study, it is concluded that LF and GM are good agriculture management practices, which promote plant growth, yield, and nutrient availability by maintaining and improving pH, enhancing available nutrients status, improving the secretion of low molecular weight organic acids, and balancing the microbial community structure in the long-term mono-cultured tea orchard.
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Guo L, Wang X, Diao T, Ju X, Zheng L, Zhang X, Han X. N 2O emission contributions by different pathways and associated microbial community dynamics in a typical calcareous vegetable soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:2005-2013. [PMID: 30061078 DOI: 10.1016/j.envpol.2018.07.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 06/18/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Nitrous oxide, one of the powerful long-lived greenhouse gases, is emitted mainly through biological processes, especially from fertilized soil. It is critical to partition the contribution of different pathways to N2O emissions and the relevant characteristics of microbial communities to identify the key N2O processes. An microcosm was conducted to partition the N2O emissions from different pathways, and the changes in soil mineral nitrogen and various nitrifiers (amoA bacteria and amoA archaea) and denitrifiers (nirS, nirK, and nosZ) were also determined using qPCR and high-throughput sequencing methods. Different gas inhibitor combinations (i.e., 0.06% acetylene, pure oxygen, 0.06% acetylene in pure oxygen, and pure helium) were used to partition the N2O pathways. A 5% oxygen treatment, with and without acetylene, was also included so that the N2O emissions could be measured under lower oxygen partial pressure. Results showed that ammonia-oxidation (AO) and successive nitrifier denitrification (NiD) were the main pathways contributing to N2O emissions at the earlier period after ammonium sulfate application with the cumulative N2O emissions accounting for 30.9% and 59.2% of the total N2O emissions, respectively. The higher NiD N2O contributions occurred when the soil nitrite concentration appeared higher, especially under the lower oxygen conditions. Higher N2O emissions from AO and NiD were associated with the compositional proportion of some dominant AOB species. Denitrification contributed more N2O (63.6%-69.3%) in the later period during incubation, coinciding with the following characteristics for denitrifiers: a) lower nosZ/(nirS + nirK) ratio, b) more diversity in nirS, and c) different proportions of some dominant species in nirK. Our results demonstrated that higher AO and successive NiD were the main N2O emission pathways, suggesting that controlling the ammonium content and weakening the AO are critical in decreasing N2O emissions.
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Affiliation(s)
- Liping Guo
- Key Lab for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xuedong Wang
- College of Resource Environment and Tourism, Capital Normal University, Beijing, 100048, China
| | - Tiantian Diao
- Key Lab for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaotang Ju
- College of Resources and Environmental Sciences, Key Lab of Plant-Soil Interaction of MOE, China Agricultural University, Beijing 100093, China
| | - Lei Zheng
- Key Lab for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Resource Environment and Tourism, Capital Normal University, Beijing, 100048, China
| | - Xinyue Zhang
- Key Lab for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xue Han
- Key Lab for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Meng J, Li J, Li J, Astals S, Nan J, Deng K, Antwi P, Xu P. The role of COD/N ratio on the start-up performance and microbial mechanism of an upflow microaerobic reactor treating piggery wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 217:825-831. [PMID: 29660708 DOI: 10.1016/j.jenvman.2018.04.029] [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: 01/18/2018] [Revised: 03/22/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
This study investigated the role of COD/N ratio on the start-up and performance of an upflow microaerobic sludge reactor (UMSR) treating piggery wastewater at 0.5 mgO2/L. At high COD/N ratio (6.24 and 4.52), results showed that the competition for oxygen between ammonia-oxidizing bacteria, nitrite-oxidizing bacteria and heterotrophic bacteria limited the removal of nitrogen. Nitrogen removal efficiency was below 40% in both scenarios. Decreasing the influent COD/N ratio to 0.88 allowed achieving high removal efficiencies for COD (∼75%) and nitrogen (∼85%) due to the lower oxygen consumption for COD mineralization. Molecular biology techniques showed that nitrogen conversion at a COD/N ratio 0.88 was dominated by the anammox pathway and that Candidatus Brocadia sp. was the most important anammox bacteria in the reactor with a relative abundance of 58.5% among the anammox bacteria. Molecular techniques also showed that Nitrosomonas spp. was the major ammonia-oxidiser bacteria (relative abundance of 86.3%) and that denitrification via NO3- and NO2- also contributed to remove nitrogen from the system.
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Affiliation(s)
- Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China; Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Jiuling Li
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China.
| | - Sergi Astals
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
| | - Kaiwen Deng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
| | - Philip Antwi
- School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
| | - Pianpian Xu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
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Angell JH, Peng X, Ji Q, Craick I, Jayakumar A, Kearns PJ, Ward BB, Bowen JL. Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment. Front Microbiol 2018; 9:170. [PMID: 29483902 PMCID: PMC5816060 DOI: 10.3389/fmicb.2018.00170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/25/2018] [Indexed: 11/13/2022] Open
Abstract
Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes (amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.
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Affiliation(s)
- John H. Angell
- Biology Department, University of Massachusetts Boston, Boston, MA, United States
| | - Xuefeng Peng
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Qixing Ji
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Ian Craick
- Biology Department, University of Massachusetts Boston, Boston, MA, United States
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Patrick J. Kearns
- Biology Department, University of Massachusetts Boston, Boston, MA, United States
| | - Bess B. Ward
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Jennifer L. Bowen
- Biology Department, University of Massachusetts Boston, Boston, MA, United States
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30
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Ding LJ, Su JQ, Sun GX, Wu JS, Wei WX. Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil. Appl Microbiol Biotechnol 2017; 102:1969-1982. [DOI: 10.1007/s00253-017-8704-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/10/2017] [Accepted: 12/11/2017] [Indexed: 01/05/2023]
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31
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Masuda Y, Itoh H, Shiratori Y, Isobe K, Otsuka S, Senoo K. Predominant but Previously-overlooked Prokaryotic Drivers of Reductive Nitrogen Transformation in Paddy Soils, Revealed by Metatranscriptomics. Microbes Environ 2017; 32:180-183. [PMID: 28442658 PMCID: PMC5478542 DOI: 10.1264/jsme2.me16179] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Waterlogged paddy soils possess anoxic zones in which microbes actively induce reductive nitrogen transformation (RNT). In the present study, a shotgun RNA sequencing analysis (metatranscriptomics) of paddy soil samples revealed that most RNT gene transcripts in paddy soils were derived from Deltaproteobacteria, particularly the genera Anaeromyxobacter and Geobacter. Despite the frequent detection of the rRNA of these microbes in paddy soils, their RNT-associated genes have rarely been identified in previous PCR-based studies. This metatranscriptomic analysis provides novel insights into the diversity of RNT microbes present in paddy soils and the ecological function of Deltaproteobacteria predominating in these soils.
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Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center
| | | | - Kazuo Isobe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Shigeto Otsuka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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32
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Gao M, Liu J, Qiao Y, Zhao M, Zhang XH. Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors. MICROBIAL ECOLOGY 2017; 73:602-615. [PMID: 27924403 DOI: 10.1007/s00248-016-0906-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 11/27/2016] [Indexed: 06/06/2023]
Abstract
Investigating the environmental influence on the community composition and abundance of denitrifiers in marine sediment ecosystem is essential for understanding of the ecosystem-level controls on the biogeochemical process of denitrification. In the present study, nirK-harboring denitrifying communities in different mud deposit zones of eastern China marginal seas (ECMS) were investigated via clone library analysis. The abundance of three functional genes affiliated with denitrification (narG, nirK, nosZ) was assessed by fluorescent quantitative PCR. The nirK-harboring microbiota were dominated by a few operational taxonomic units (OTUs), which were widely distributed in different sites with each site harboring their unique phylotypes. The mean abundance of nirK was significantly higher than that of narG and nosZ genes, and the abundance of narG was higher than that of nosZ. The inconsistent abundance profile of different functional genes along the process of denitrification might indicate that nitrite reduction occurred independently of denitrification in the mud deposit zones of ECMS, and sedimentary denitrification was accomplished by cooperation of different denitrifying species rather than a single species. Such important information would be missed when targeting only a single denitrifying functional gene. Analysis of correlation between abundance ratios and environmental factors revealed that the response of denitrifiers to environmental factors was not invariable in different mud deposit zones. Our results suggested that a comprehensive analysis of different denitrifying functional genes may gain more information about the dynamics of denitrifying microbiota in marine sediments.
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Affiliation(s)
- Minghong Gao
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Yanlu Qiao
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Meixun Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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Zhang Z, Zhang W, Yang H, Sheng R, Wei W, Qin H. Elevated N 2O emission by the rice roots: based on the abundances of narG and bacterial amoA genes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:2116-2125. [PMID: 27812967 DOI: 10.1007/s11356-016-7993-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 10/25/2016] [Indexed: 06/06/2023]
Abstract
Rice fields are an important source of nitrous oxide (N2O), where rice plants could act as a key factor controlling N2O fluxes during the flooding-drying process; however, the microbial driving mechanisms are unclear. In this study, specially designed equipment was used to grow rice plants and collect emitted N2O from the root-growing zone (zone A), root-free zones (zones B, C, and D) independently, at tillering and booting stages under flooding and drying conditions. Soil samples from the four zones were also taken separately. Nitrifying and denitrifying community abundances were detected using quantitative polymerase chain reaction (qPCR). The N2O emission increased significantly along with drying, but the N2O emission capabilities varied among the four zones under drying, while zone B possessed the highest N2O fluxes that were 2.7~4.5 times higher than those from zones C and D. However, zone A showed N2O consumption potential. Notably, zone B also harbored the highest numbers of narG-containing denitrifiers and amoA-containing nitrifiers under drying at both tillering and booting stages. This study demonstrates that drying caused significant increase in N2O emission from rhizosphere soil, in which the higher abundance of AOB would help to produce more nitrate and significantly higher narG-containing microbes would drive more N2O production and emission.
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Affiliation(s)
- Zhenxing Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenzhao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Huicui Yang
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rong Sheng
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Wenxue Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Hongling Qin
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China.
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Wang H, Yang SH, Yang JP, Lv YM, Zhao X, Pang JL. Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards. J Zhejiang Univ Sci B 2015; 15:953-65. [PMID: 25367788 DOI: 10.1631/jzus.b1400114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle.
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Affiliation(s)
- Hua Wang
- Institute of Environmental Protection, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
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Wang N, Ding LJ, Xu HJ, Li HB, Su JQ, Zhu YG. Variability in responses of bacterial communities and nitrogen oxide emission to urea fertilization among various flooded paddy soils. FEMS Microbiol Ecol 2015; 91:fiv013. [DOI: 10.1093/femsec/fiv013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2015] [Indexed: 11/12/2022] Open
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36
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Su JQ, Ding LJ, Xue K, Yao HY, Quensen J, Bai SJ, Wei WX, Wu JS, Zhou J, Tiedje JM, Zhu YG. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Mol Ecol 2014; 24:136-50. [DOI: 10.1111/mec.13010] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/13/2014] [Accepted: 11/17/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Jian-Qiang Su
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 China
| | - Long-Jun Ding
- State Key Lab of Urban and Regional Ecology; Research Center for Eco-environmental Sciences; Chinese Academy of Sciences; Beijing 100085 China
| | - Kai Xue
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; 101 David L Boren Blvd Norman OK 73019 USA
| | - Huai-Ying Yao
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 China
| | - John Quensen
- Center for Microbial Ecology; Department of Plant, Soil and Microbial Sciences; Michigan State University; East Lansing MI 48824 USA
| | - Shi-Jie Bai
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; 101 David L Boren Blvd Norman OK 73019 USA
| | - Wen-Xue Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-ecology Research; Institute of Subtropical Agriculture; Chinese Academy of Sciences; Changsha 410125 China
| | - Jin-Shui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-ecology Research; Institute of Subtropical Agriculture; Chinese Academy of Sciences; Changsha 410125 China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; 101 David L Boren Blvd Norman OK 73019 USA
- Earth Science Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control; School of Environment; Tsinghua University; Beijing 100084 China
| | - James M. Tiedje
- Center for Microbial Ecology; Department of Plant, Soil and Microbial Sciences; Michigan State University; East Lansing MI 48824 USA
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 China
- State Key Lab of Urban and Regional Ecology; Research Center for Eco-environmental Sciences; Chinese Academy of Sciences; Beijing 100085 China
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Kathiravan V, Krishnani KK. Pseudomonas aeruginosa and Achromobacter sp.: nitrifying aerobic denitrifiers have a plasmid encoding for denitrifying functional genes. World J Microbiol Biotechnol 2013; 30:1187-98. [DOI: 10.1007/s11274-013-1543-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 10/22/2013] [Indexed: 10/26/2022]
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38
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Distribution of Hydrocarbon-Degrading Bacteria in the Soil Environment and Their Contribution to Bioremediation. Appl Biochem Biotechnol 2013; 170:329-39. [DOI: 10.1007/s12010-013-0170-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 02/28/2013] [Indexed: 11/26/2022]
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39
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Velusamy K, Krishnani KK. Heterotrophic Nitrifying and Oxygen Tolerant Denitrifying Bacteria from Greenwater System of Coastal Aquaculture. Appl Biochem Biotechnol 2013; 169:1978-92. [DOI: 10.1007/s12010-013-0109-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
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40
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Jung J, Choi S, Jung H, Scow KM, Park W. Primers for amplification of nitrous oxide reductase genes associated with Firmicutes and Bacteroidetes in organic-compound-rich soils. MICROBIOLOGY-SGM 2012. [PMID: 23197174 DOI: 10.1099/mic.0.060194-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The nosZ gene encodes nitrous oxide reductase, a key enzyme in the nitrous oxide reduction that occurs during complete denitrification. Many conventional approaches have used Proteobacteria-based primers to detect nosZ in environmental samples. However, these primers often fail to detect nosZ in non-Proteobacteria strains, including Firmicutes (Gram-positive) and Bacteroidetes. In this study, newly designed nosZ primers successfully amplified this gene from five Geobacillus species (Firmicutes). The primers were used to construct nosZ clone libraries from DNA extracted from sludge and domestic animal feedlot soils, all with high organic carbon contents. After DNA sequencing, phylogenetic analysis identified many new nosZ sequences with high levels of homology to nosZ from Bacteroidetes, probably because of the high sequence similarity of nosZ from Firmicutes and Bacteroidetes, and a predominance of Bacteroidetes in feedlot environments. Three sets of new quantitative real-time PCR (qPCR) primers based on our clone library sequences were designed and tested for their specificities. Our data showed that only Bacteroidetes-related nosZ sequences were amplified, whereas conventional Proteobacteria-based primers amplified only Proteobacteria-related nosZ. Quantitative analysis of nosZ with the new qPCR primers recovered ~10(4) copies per 100 ng DNA. Thus, it appears that amplification with conventional primers is insufficient for developing an understanding of the diversity and abundance of nosZ genes in the environment.
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Affiliation(s)
- Jaejoon Jung
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Sungjong Choi
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Hoon Jung
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Kate M Scow
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Woojun Park
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
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Ahn JH, Song J, Kim BY, Kim MS, Joa JH, Weon HY. Characterization of the bacterial and archaeal communities in rice field soils subjected to long-term fertilization practices. J Microbiol 2012; 50:754-65. [PMID: 23124742 DOI: 10.1007/s12275-012-2409-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 09/26/2012] [Indexed: 12/23/2022]
Abstract
The bacterial and archaeal communities in rice field soils subjected to different fertilization regimes for 57 years were investigated in two different seasons, a non-planted, drained season (April) and a rice-growing, flooded season (August), by performing soil dehydrogenase assay, real-time PCR assay and pyrosequencing analysis. All fertilization regimes increased the soil dehydrogenase activity while the abundances of bacteria and archaea increased in the plots receiving inorganic fertilizers plus compost and not in those receiving inorganic fertilizers only. Rice-growing and flooding decreased the soil dehydrogenase activity while they increased the bacterial diversity in rice field soils. The bacterial communities were dominated by Chloroflexi, Proteobacteria, and Actinobacteria and the archaeal communities by Crenarchaeota at the phylum level. In principal coordinates analysis based on the weighted Fast UniFrac metric, the bacterial and archaeal communities were separated primarily by season, and generally distributed along with soil pH, the variation of which had been caused by long-term fertilization. Variations in the relative abundance according to the season or soil pH were observed for many bacterial and archaeal groups. In conclusion, the microbial activity, prokaryotic abundance and diversity, and prokaryotic community structure in the rice field soils were changed by season and long-term fertilization.
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Affiliation(s)
- Jae-Hyung Ahn
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
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