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Gao F, Li Y, Fan H, Luo D, Chapman SJ, Yao H. 15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils. Appl Microbiol Biotechnol 2024; 108:342. [PMID: 38789552 PMCID: PMC11126484 DOI: 10.1007/s00253-024-13170-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: 10/06/2023] [Revised: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3--N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different.
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Affiliation(s)
- Fuyun Gao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
| | - Haoxin Fan
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430073, People's Republic of China
| | - Dan Luo
- College of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, People's Republic of China
| | | | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430073, People's Republic of China.
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Feng M, Lin Y, He ZY, Hu HW, Jin S, Liu J, Wan S, Cheng Y, He JZ. Higher stochasticity in comammox Nitrospira community assembly in upland soils than the adjacent paddy soils at a regional scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171227. [PMID: 38402820 DOI: 10.1016/j.scitotenv.2024.171227] [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: 12/04/2023] [Revised: 01/22/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024]
Abstract
Understanding the assembly mechanisms of microbial communities, particularly comammox Nitrospira, in agroecosystems is crucial for sustainable agriculture. However, the large-scale distribution and assembly processes of comammox Nitrospira in agricultural soils remain largely elusive. We investigated comammox Nitrospira abundance, community structure, and assembly processes in 16 paired upland peanuts and water-logged paddy soils in south China. Higher abundance, richness, and network complexity of comammox Nitrospira were observed in upland soils than in paddy soils, indicating a preference for upland soils over paddy soils among comammox Nitrospira taxa in agricultural environments. Clade A.2.1 and clade A.1 were the predominant comammox Nitrospira taxa in upland and paddy soils, respectively. Soil pH was the most crucial factor shaping comammox Nitrospira community structure. Stochastic processes were found to predominantly drive comammox Nitrospira community assembly in both upland and paddy soils, with deterministic processes playing a more important role in paddy soils than in upland soils. Overall, our findings demonstrate the higher stochasticity of comammox Nitrospira in upland soils than in the adjacent paddy soils, which may have implications for autotrophic nitrification in acidic agricultural soils.
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Affiliation(s)
- Mengmeng Feng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Yongxin Lin
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China.
| | - Zi-Yang He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, VIC 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, VIC 3010, Australia
| | - Shengsheng Jin
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Jia Liu
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Song Wan
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Yuheng Cheng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Ji-Zheng He
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China; School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, VIC 3010, Australia.
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3
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Zhao Y, Ling N, Liu X, Li C, Jing X, Hu J, Rui J. Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate. Appl Environ Microbiol 2024; 90:e0007024. [PMID: 38385702 DOI: 10.1128/aem.00070-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.
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Affiliation(s)
- Yuwei Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ning Ling
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Chao Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xin Jing
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jingjing Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Junpeng Rui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Huda N, Rana MR, Huq MA, Al-Mamun A, Rahman ST, Alam MK, Rahman MM. Understanding vermicompost and organic manure interactions: impact on toxic elements, nitrification activity, comammox Nitrospira inopinata, and archaea/bacteria. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:355. [PMID: 38466496 DOI: 10.1007/s10661-024-12491-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/19/2024] [Indexed: 03/13/2024]
Abstract
Vermicompost is a substantial source of nutrients, promotes soil fertility, and maintains or increases soil organic matter levels. Potentially toxic elements (PTEs) in vermicompost impact on nitrification activity. However, it is yet unknown how vermicompost affects nitrifying bacteria and archaea, comammox Nitrospira inopinata (complete ammonia oxidizers), net nitrification rates (NNRs), and PTEs. The effects of vermicompost application on NNRs, potential nitrification rates (NPs), PTEs, and the abundances of comammox N. inopinata bacteria, nitrite-oxidizing bacteria (NOB), and ammonia-oxidizing bacteria (AOB)/archaea (AOA) were studied. NNRs and NPs were significantly higher (p < 0.05) in fresh cow-dung vermicompost (stored for 40 days) as compared with other organic manure. The level of PTEs (Cu2+, Fe2+, Pb2+, Cd2+, and Zn2+) was significantly lower (p < 0.05) in vermicompost as compared with compost of waste material with Trichoderma and cow dung. Comammox N. inopinata, NOB, AOB, and AOA were significantly higher (p < 0.05) in stored cow-dung vermicompost (more than 1 year) as compared with other organic manure. The results of the scatterplot matrix analysis suggested that Fe2+, total nitrogen (TN), soil organic carbon (SOC), and total carbon (TC) were linearly correlated (p < 0.001) with NNRs and NPs in vermicompost and organic manure. Similarly, comammox N. inopinata bacteria, NOB, AOB, and AOA were linearly correlated (p < 0.001) with NNR and NP. These results indicated that vermicompost promoted nitrification activity by increasing microbial diversity and abundance, supplying nutrients and organic matter for microbial growth, and facilitating complex microbial interactions. It may be concluded that the influence of vermicompost, which played a great role in PTE concentration reduction, increased chemical, and biological properties, increased the growth rate of nitrifying bacteria/archaea and the nitrogen cycle.
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Affiliation(s)
- Nazmul Huda
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Rasel Rana
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong-Si, Gyeonggi-Do, 17546, Republic of Korea
| | - Abdullah Al-Mamun
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Shabiha Tasbir Rahman
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Khasrul Alam
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - M Mizanur Rahman
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh.
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Chen Y, Fu W, Xiao H, Zhai Y, Luo Y, Wang Y, Liu Z, Li Q, Huang J. A Review on Rhizosphere Microbiota of Tea Plant ( Camellia sinensis L): Recent Insights and Future Perspectives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19165-19188. [PMID: 38019642 DOI: 10.1021/acs.jafc.3c02423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Rhizosphere microbial colonization of the tea plant provides many beneficial functions for the host, But the factors that influence the composition of these rhizosphere microbes and their functions are still unknown. In order to explore the interaction between tea plants and rhizosphere microorganisms, we summarized the current studies. First, the review integrated the known rhizosphere microbial communities of tea tree, including bacteria, fungi, and arbuscular mycorrhizal fungi. Then, various factors affecting tea rhizosphere microorganisms were studied, including: endogenous factors, environmental factors, and agronomic practices. Finally, the functions of rhizosphere microorganisms were analyzed, including (a) promoting the growth and quality of tea trees, (b) alleviating biotic and abiotic stresses, and (c) improving soil fertility. Finally, we highlight the gaps in knowledge of tea rhizosphere microorganisms and the future direction of development. In summary, understanding rhizosphere microbial interactions with tea plants is key to promoting the growth, development, and sustainable productivity of tea plants.
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Affiliation(s)
- Yixin Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Wenjie Fu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Han Xiao
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yuke Zhai
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Sciences, Zhejiang University, Hangzhou, Zhejiang 3100058, P.R. China
| | - Yingzi Wang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Zhonghua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Qin Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
- Institute of Soil and Water Resources and Environmental Sciences, Zhejiang University, Hangzhou, Zhejiang 3100058, P.R. China
| | - Jianan Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
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Wang M, Wu S, Lu Y, Wu H, Si D, Zhou D. Combined application of strong alkaline materials and specific organic fertilizer accelerates nitrification process of a rare earth mining soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163042. [PMID: 36965722 DOI: 10.1016/j.scitotenv.2023.163042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/02/2023] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
Abstract
The extensive usage of ammonium sulfate as the leaching agent to extract rare earth elements led to widespread ammonia nitrogen (NH4+-N) pollution in the tailing soils of ion-adsorbed rare earth deposits in southern China. However, the cost-effective technologies to tackle with the long-term retention of NH4+-N in the rare earth mining soil have been largely unresolved. In this study, we developed a cost-effective approach to activate soil nitrification by the co-application of alkaline materials and organic fertilizer. The co-application of 0.3 % of organic fertilizer and 0.1 % ∼ 0.2 % of CaO or MgO or Mg(OH)2 stimulated a soil NH4+-N decrease rate of 2.01-7.58 mg kg-1 d-1 and a soil NO3--N accumulation rate of 1.56-7.09 mg kg-1 d-1. Noting that only if the soil pH was elevated to 7.81-9.00, the NH4+-N decrease rate and NO3--N accumulation rate were dependent on the proton consumption capacity of the alkaline materials. The application of CaCO3 could not stimulate soil nitrification possibly due to the soil pH was uncapable to be elevated to above 7.68. The qPCR, amplicon sequencing, and nitrification inhibitor batch incubation results demonstrated that organic fertilizer supplied active ammonia-oxidizing bacteria Nitrosomonas europaea. The proliferation of Nitrosomonas europaea in the alkaline materials and organic fertilizer co-applied soil was responsible for the soil nitrification. Furthermore, the application of commercial denitrifying bacteria inoculum promoted the removal of accumulated NO3--N. The findings of this study provide a lost-cost technology to remove NH4+-N from the rare earth mining soil.
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Affiliation(s)
- Min Wang
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Song Wu
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Yilin Lu
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Haotian Wu
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Dunfeng Si
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Dongmei Zhou
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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Wang Y, Zeng X, Zhang Y, Zhang N, Xu L, Wu C. Responses of potential ammonia oxidation and ammonia oxidizers community to arsenic stress in seven types of soil. J Environ Sci (China) 2023; 127:15-29. [PMID: 36522049 DOI: 10.1016/j.jes.2022.02.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 06/17/2023]
Abstract
Soil arsenic contamination is of great concern because of its toxicity to human, crops, and soil microorganisms. However, the impacts of arsenic on soil ammonia oxidizers communities remain unclear. Seven types of soil spiked with 0 or 100 mg arsenic per kg soil were incubated for 180 days and sampled at days 1, 15, 30, 90 and 180. The changes in the community composition and abundance of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, clone library sequencing, and quantitative PCR (qPCR) targeting amoA gene. Results revealed considerable variations in the potential ammonia oxidation (PAO) rates in different soils, but soil PAO was not consistently significantly inhibited by arsenic, probably due to the low bioavailable arsenic contents or the existence of functional redundancy between AOB and AOA. The variations in AOB and AOA communities were closely associated with the changes in arsenic fractionations. The amoA gene abundances of AOA increased after arsenic addition, whereas AOB decreased, which corroborated the notion that AOA and AOB might occupy different niches in arsenic-contaminated soils. Phylogenetic analysis of amoA gene-encoded proteins revealed that all AOB clone sequences belonged to the genus Nitrosospira, among which those belonging to Nitrosospira cluster 3a were dominant. The main AOA sequence detected belonged to Thaumarchaeal Group 1.1b, which was considered to have a high ability to adapt to environmental changes. Our results provide new insights into the impacts of arsenic on the soil nitrogen cycling.
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Affiliation(s)
- Yanan Wang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Xibai Zeng
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China.
| | - Yang Zhang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Nan Zhang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Liyang Xu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Cuixia Wu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
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Ren BJ, Shen LD, Liu X, Jin JH, Huang HC, Tian MH, Yang YL, Yang WT, Liu JQ, Geng CY, Wu HS, Hu ZH. Effect of gradual increase of atmospheric CO 2 concentration on nitrification potential and communities of ammonia oxidizers in paddy fields. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116597. [PMID: 36308785 DOI: 10.1016/j.jenvman.2022.116597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/18/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Currently, the influence of elevated atmospheric CO2 concentration (eCO2) on ammonia oxidation to nitrite, the rate-limiting step of nitrification in paddy soil, is poorly known. Previous studies that simulate the effect of eCO2 on nitrification are primarily based on an abrupt increase of atmospheric CO2 concentration. However, paddy ecosystems are experiencing a gradual increase of CO2 concentration. To better understand how the nitrification potential, abundance and communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) respond to eCO2 in paddy ecosystems, a field experiment was conducted using the following two treatments: a gradual increase of CO2 (EC, increase of 40 ppm per year until 200 ppm above ambient) and ambient CO2 (CK). The results demonstrated that the EC treatment significantly (P < 0.05) stimulated the soil potential nitrification rate (PNR) at the jointing and milky stages, which increased by 127.83% and 27.35%, respectively, compared with CK. Furthermore, the EC treatment significantly (P < 0.05) stimulated the AOA and AOB abundance by 56.60% and 133.84%, respectively, at the jointing stage. Correlation analysis showed that the PNR correlated well with the abundance of AOB (R2 = 0.7389, P < 0.001). In addition, the EC treatment significantly (P < 0.05) altered the community structure of AOB, while it had little effect on that of AOA. A significant difference in the proportion of Nitrosospira was observed between CO2 treatments. In conclusion, the gradual increase of CO2 positively influenced the PNR and abundance of ammonia oxidizers, and AOB could be more important than AOA in nitrification under eCO2.
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Affiliation(s)
- Bing-Jie Ren
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Xin Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jing-Hao Jin
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - He-Chen Huang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Mao-Hui Tian
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yu-Ling Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Wang-Ting Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jia-Qi Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Cai-Yu Geng
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hong-Sheng Wu
- Department of Agricultural Resources and Environment, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Zheng-Hua Hu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China.
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9
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The contributions of ammonia oxidizing bacteria and archaea to nitrification-dependent N 2O emission in alkaline and neutral purple soils. Sci Rep 2022; 12:19928. [PMID: 36402873 PMCID: PMC9675842 DOI: 10.1038/s41598-022-23084-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/25/2022] [Indexed: 11/21/2022] Open
Abstract
Nitrification is believed to be one of the primary processes of N2O emission in the agroecological system, which is controlled by soil microbes and mainly regulated by soil pH, oxygen content and NH4+ availability. Previous studies have proved that the relative contributions of ammonia oxidizing bacteria (AOB) and archaea (AOA) to N2O production were varied with soil pH, however, there is still no consensus on the regulating mechanism of nitrification-derived N2O production by soil pH. In this study, 1-octyne (a selective inhibitor of AOB) and acetylene (an inhibitor of AOB and AOA) were used in a microcosm incubation experiment to differentiate the relative contribution of AOA and AOB to N2O emissions in a neutral (pH = 6.75) and an alkaline (pH = 8.35) soils. We found that the amendment of ammonium (NH4+) observably stimulated the production of both AOA and AOB-related N2O and increased the ammonia monooxygenase (AMO) gene abundances of AOA and AOB in the two test soils. Among which, AOB dominated the process of ammonia oxidation in the alkaline soil, contributing 70.8% of N2O production derived from nitrification. By contrast, the contribution of AOA and AOB accounted for about one-third of nitrification-related N2O in acidic soil, respectively. The results indicated that pH was a key factor to change abundance and activity of AOA and AOB, which led to the differentiation of derivation of N2O production in purple soils. We speculate that both NH4+ content and soil pH mediated specialization of ammonia-oxidizing microorganisms together; and both specialization results and N2O yield led to the different N2O emission characteristics in purple soils. These results may help inform the development of N2O reduction strategies in the future.
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Mishra S, Wang W, Xia S, Lin L, Yang X. Spatial pattern of functional genes abundance reveals the importance of PhoD gene harboring bacterial community for maintaining plant growth in the tropical forest of Southwestern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156863. [PMID: 35750182 DOI: 10.1016/j.scitotenv.2022.156863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The concept of microbial functional genes has added a new dimension to microbial ecology research by improving the model of microbial community-ecosystem functions relationship. However, our knowledge vis-à-vis fine-scale spatial distribution pattern of functional genes and their probable impact on plant community in the hyper-diverse tropical forest ecosystem is very limited. Here, we investigated the spatial pattern of functional genes abundance (NirK, AOA, AOB, and PhoD), identified key influencing factors, and distinguished the key functional group supporting the plant community in a tropical rainforest located in Xishuangbanna. In total, 200 soil samples and vegetation data of ~4800 individuals of plants across a 1 ha study area were collected. Our results detected higher spatial variability with a maximum magnitude of abundance for PhoD gene (4.53 × 107 copies) followed by NirK (2.71 × 106 copies), AOA (1.97 × 106 copies), and AOB (7.38 × 104 copies). A strong spatial dependence was observed for PhoD and NirK over the distance of 17 and 18 m, respectively. Interestingly, the N:P stoichiometry played a critical role in structuring the spatial pattern of the most abundant PhoD gene. The significant positive and negative relationship of PhoD with N:P ratio and available phosphorus, respectively, indicated that the P-limiting environment was a driving factor for recruitment of PhoD gene community. The structural equation modeling ascertained the direct positive impact of PhoD on plant biomass and high demand of available P by plants suggesting that the organic phosphorus mineralization process is essential to maintain plant productivity by re-establishing the availability of the most limiting P nutrient. Our preliminary study improves our understanding of how microbial functional genes-environment associations could be used for monitoring soil health and its overall impact on ecosystem multifunctionality. Finally, we intend to conduct the study at a large spatial scale for achieving a holistic view.
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Affiliation(s)
- Sandhya Mishra
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Wenting Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Shangwen Xia
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Luxiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan 665000, China.
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Zhang X, Shan X, Fu H, Sun Z. Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions. PeerJ 2022; 10:e14088. [PMID: 36213504 PMCID: PMC9536323 DOI: 10.7717/peerj.14088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/29/2022] [Indexed: 01/20/2023] Open
Abstract
Background Nitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification. Materials and Methods A simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively. Results and discussions Soil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4 + content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA. Conclusions PNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4 +, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.
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Akter R, Mukhles MB, Rahman MM, Rana MR, Huda N, Ferdous J, Rahman F, Rafi MH, Biswas SK. Effect of pesticides on nitrification activity and its interaction with chemical fertilizer and manure in long-term paddy soils. CHEMOSPHERE 2022; 304:135379. [PMID: 35716712 DOI: 10.1016/j.chemosphere.2022.135379] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Effect of pesticides on nitrification activity and its interaction among heavy metal concentrations (HMCs), antibiotic resistance genes (ARGs), and ammonia monooxygenase (amoA) genes of long-term paddy soils is little known. The aim was to study the effect of pesticides on net nitrification rate (NR), potential nitrification rate (NP), HMCs, ARGs (sulI, sulII, tetO, and tetQ), and amoA (amoA-AOA, amoA-AOB, and amoA-NOB) genes in long-term treated paddy soils. NR and NP were significantly decreased (p < 0.05), whereas HMCs (Pb2+, Cu2+, Zn2+, and Fe3+) were a significantly increased (p < 0.05) in chemical fertilizer with pesticide treated paddy soils as compared with chemical fertilizer treated paddy soils. The scatter plot matrix indicated that total carbon (TC), soil organic carbon (SOC), total nitrogen (TN), and Fe were linearly correlated with NR and NP in long-term treated paddy soils. ARGs and amoA genes were significantly decreased (p < 0.05) in chemical fertilizer and manure with pesticide treated paddy soils. Overall, the result indicated the response of pesticide and their combination of manure with pesticide interaction present in long-term paddy soils, which will play a great role in the control uses of pesticides, manure, and chemical fertilizers in paddy soils and protect the nitrogen cycle as well as environment.
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Affiliation(s)
- Rehena Akter
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Muntaha Binte Mukhles
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh.
| | - Md Rasel Rana
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Nazmul Huda
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Jannatul Ferdous
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Fahida Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Meherab Hossain Rafi
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Sudhangshu Kumar Biswas
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
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Farooq MS, Wang X, Uzair M, Fatima H, Fiaz S, Maqbool Z, Rehman OU, Yousuf M, Khan MR. Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system. FRONTIERS IN PLANT SCIENCE 2022; 13:960641. [PMID: 36092421 PMCID: PMC9453445 DOI: 10.3389/fpls.2022.960641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa L.) is considered as a staple food for more than half of the global population, and sustaining productivity under a scarcity of resources is challenging to meet the future food demands of the inflating global population. The aerobic rice system can be considered as a transformational replacement for traditional rice, but the widespread adaptation of this innovative approach has been challenged due to higher losses of nitrogen (N) and reduced N-use efficiency (NUE). For normal growth and developmental processes in crop plants, N is required in higher amounts. N is a mineral nutrient and an important constituent of amino acids, nucleic acids, and many photosynthetic metabolites, and hence is essential for normal plant growth and metabolism. Excessive application of N fertilizers improves aerobic rice growth and yield, but compromises economic and environmental sustainability. Irregular and uncontrolled use of N fertilizers have elevated several environmental issues linked to higher N losses in the form of nitrous oxide (N2O), ammonia (NH3), and nitrate (NO3 -), thereby threatening environmental sustainability due to higher warming potential, ozone depletion capacities, and abilities to eutrophicate the water resources. Hence, enhancing NUE in aerobic rice has become an urgent need for the development of a sustainable production system. This article was designed to investigate the major challenge of low NUE and evaluate recent advances in pathways of the N cycle under the aerobic rice system, and thereby suggest the agronomic management approaches to improve NUE. The major objective of this review is about optimizing the application of N inputs while sustaining rice productivity and ensuring environmental safety. This review elaborates that different soil conditions significantly shift the N dynamics via changes in major pathways of the N cycle and comprehensively reviews the facts why N losses are high under the aerobic rice system, which factors hinder in attaining high NUE, and how it can become an eco-efficient production system through agronomic managements. Moreover, it explores the interactive mechanisms of how proper management of N cycle pathways can be accomplished via optimized N fertilizer amendments. Meanwhile, this study suggests several agricultural and agronomic approaches, such as site-specific N management, integrated nutrient management (INM), and incorporation of N fertilizers with enhanced use efficiency that may interactively improve the NUE and thereby plant N uptake in the aerobic rice system. Additionally, resource conservation practices, such as plant residue management, green manuring, improved genetic breeding, and precision farming, are essential to enhance NUE. Deep insights into the recent advances in the pathways of the N cycle under the aerobic rice system necessarily suggest the incorporation of the suggested agronomic adjustments to reduce N losses and enhance NUE while sustaining rice productivity and environmental safety. Future research on N dynamics is encouraged under the aerobic rice system focusing on the interactive evaluation of shifts among activities and diversity in microbial communities, NUE, and plant demands while applying N management measures, which is necessary for its widespread adaptation in face of the projected climate change and scarcity of resources.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Hira Fatima
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
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Sun X, Zhao J, Zhang L, Zhou X, Xia W, Zhao Y, Jia Z. Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155568. [PMID: 35490817 DOI: 10.1016/j.scitotenv.2022.155568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/19/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such variation is mostly limited to ammonia oxidizers (AO) in local fields, excluding soil heterogeneity and nitrite-oxidizing bacteria (NOB); the variation under diverse climatic and soil conditions is not comprehensively understood. We conducted a large-scale survey of 131 cropland and natural sites in China. The community patterns of ammonia-oxidizing bacteria (AOB) and NOB differed significantly between croplands and some natural ecosystems, whereas ammonia-oxidizing archaea (AOA) were not affected by ecosystem type. The AOB population and nitrification potential (NP) were significantly higher in agroecosystems than in natural systems except wetlands. Fewer co-occurrence interactions involving nitrifiers were observed in croplands than in natural ecosystems except forests, systematically indicating the ecological diversification of nitrifiers in potential microbial associations among these habitats. Ecosystem type, pH, organic matter (OM), total phosphorus (TP), mean annual temperature (MAT) and mean annual precipitation (MAP) were primary drivers of nitrifier community and functional shifts. This study provides the first large-scale evidence of overall nitrifier community (i.e., AOA, AOB and NOB) and potential functional shifts between agroecosystems and natural environments, enabling predictions of terrestrial N cycle under foreseeable natural land use conversions and global climate change.
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Affiliation(s)
- Xiangxin Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu Province, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Zhao
- Institute for Food and Agricultural Sciences (IFAS), Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie 33314, FL, USA
| | - Liyan Zhang
- College of Environment, Hohai University, Nanjing 210098, Jiangsu Province, China
| | - Xue Zhou
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, Jiangsu Province, China
| | - Weiwei Xia
- College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, Jiangsu Province, China
| | - Yuguo Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu Province, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu Province, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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15
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Zhang Z, Yu Z, Zhang Y, Shi Y. Impacts of Fertilization Optimization on Soil Nitrogen Cycling and Wheat Nitrogen Utilization Under Water-Saving Irrigation. FRONTIERS IN PLANT SCIENCE 2022; 13:878424. [PMID: 35665172 PMCID: PMC9161168 DOI: 10.3389/fpls.2022.878424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Scholars have proposed the practice of split nitrogen fertilizer application (SNFA), which has proven to be an effective approach for enhancing nitrogen use efficiency. However, the combined effects of SNFA on wheat plant nitrogen use efficiency, ammonia (NH3) emission flux, as well as the rates of nitrification and denitrification in different ecosystems remain unclear. Meanwhile, few studies have sought to understand the effects of the split nitrogen fertilizer method under water-saving irrigation technology conditions on nitrogen loss. The current study assessed soil NH3 volatilization, nitrification, and denitrification intensities, as well as the abundance of nitrogen cycle-related functional genes following application of different treatments. Specifically, we applied a nitrogen rate of 240 kg⋅ha-1, and the following fertilizer ratios of the percent base to that of topdressing under water-saving irrigation: N1 (basal/dressing, 100/0%), N2 (basal/dressing, 70/30%), N3 (basal/dressing, 50/50%), N4 (basal/dressing, 30/70%), and N5 (basal/dressing, 0/100%). N3 treatment significantly reduced NH3 volatilization, nitrification, and denitrification intensities, primarily owing to the reduced reaction substrate concentration (NO3 - and NH4 +) and abundance of functional genes involved in the nitrogen cycle (amoA-AOB, nirK, and nirS) within the wheat-land soil. 15N tracer studies further demonstrated that N3 treatments significantly increased the grain nitrogen accumulation by 9.50-28.27% compared with that under other treatments. This increase was primarily due to an increase in the amount of nitrogen absorbed by wheat from soil and fertilizers, which was caused by an enhancement in total nitrogen uptake (7.2-21.81%). Overall, N3 treatment (basal/dressing, 50/50%) was found to effectively reduce nitrogen loss through NH3 volatilization, nitrification and denitrification while improving nitrogen uptake by wheat. Thus, its application will serve to further maximize the yield and provide a fertilization practice that will facilitate cleaner wheat production in the North China Plain.
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Zheng J, Tao L, Dini-Andreote F, Luan L, Kong P, Xue J, Zhu G, Xu Q, Jiang Y. Dynamic Responses of Ammonia-Oxidizing Archaea and Bacteria Populations to Organic Material Amendments Affect Soil Nitrification and Nitrogen Use Efficiency. Front Microbiol 2022; 13:911799. [PMID: 35633707 PMCID: PMC9135446 DOI: 10.3389/fmicb.2022.911799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
Organic material amendments have been proposed as an effective strategy to promote soil health by enhancing soil fertility and promoting nitrogen (N) cycling and N use efficiency (NUE). Thus, it is important to investigate the extent to which the structure and function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) differentially respond to the organic material amendments in field settings. Here, we conducted a 9-year field experiment to track the responses of AOA and AOB populations to the organic material amendments and measured the potential nitrification activity (PNA), plant productivity, and NUE in the plant rhizosphere interface. Our results revealed that the organic material amendments significantly enhanced the abundance and diversity of AOA and AOB populations. Further, significant differences were observed in the composition and co-occurrence network of AOA and AOB. A higher occurrence of potential competitive interactions between taxa and enumerated potential keystone taxa was observed in the AOA-AOB network. Moreover, we found that AOA was more important than AOB for PNA under the organic material amendments. Structural equation modeling suggested that the diversity of AOA and AOB populations induced by the potential competitive interactions with keystone taxa dynamically accelerated the rate of PNA, and positively affected plant productivity and NUE under the organic material amendments. Collectively, our study offers new insights into the ecology and functioning of ammonia oxidizers and highlights the positive effects of organic material amendments on nitrogen cycling dynamics.
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Affiliation(s)
- Jie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liang Tao
- Guangdong Key Laboratory of Integrated Agroenvironmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Peijun Kong
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingrong Xue
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Guofan Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Qinsong Xu
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- *Correspondence: Yuji Jiang,
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Ye H, Tang C, Cao Y, Li X, Huang P. Contribution of ammonia-oxidizing archaea and bacteria to nitrification under different biogeochemical factors in acidic soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:17209-17222. [PMID: 34661841 DOI: 10.1007/s11356-021-16887-8] [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: 07/07/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Nitrification in soils is an essential process that involves archaeal and bacterial ammonia-oxidizers. Despite its importance, the relative contributions of soil factors to the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their nitrification performances are seldom discussed. The aim of this study was to determine the effects of AOA and AOB abundance and different environmental conditions (pH, TC, TN, moisture, and temperature) on nitrification performance. The soils of the long-term fertilized tea orchards and forests were sampled in the field, and nitrification experiments were conducted in the laboratory. The acid soils were collected from the field and used in laboratory incubation experiments to calculate the nitrification rate, including the net nitrification rate (NN rate), nitrification potential (NP), and nitrification kinetics. The basic parameters, different forms of nitrogen content, and AOA and AOB amoA gene copies were also analyzed. Compared with the forest soil, the tea orchard soil had a lower pH and higher nitrogen content (p < 0.05). The AOA and AOB abundance in the soils of the forests and tea orchards were pH-dependent. The NN rate and NP had good relationships with AOA or AOB in the forest soil; however, poor relationships were observed in the tea orchard soil. When pH < 4, the performances of AOA and AOB were restricted by pH and the environment, especially in long-term fertilized farmlands. Long-term fertilization can cause soil acidification, which regulates the abundance of AOA and AOB and their nitrifying ability. The soil environment rather than AOA or AOB could control nitrification in long-term fertilized farmlands with a pH below 4. These findings could improve fertilization efficiency and control nutrient runoff in hilly agricultural ecosystems.
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Affiliation(s)
- Huijun Ye
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510006, China
| | - Changyuan Tang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510006, China
- School of Geography and Planning, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yingjie Cao
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510006, China.
- Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China.
| | - Xing Li
- Wuhan Institute of Technology, Wuhan, 430000, China
| | - Pinyi Huang
- School of Geography and Planning, Sun Yat-Sen University, Guangzhou, 510006, China
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He F, Yu H, Liu D, Li Z. Microorganism community composition analysis coupling with 15N tracer experiments reveals the nitrification rate and N2O emissions in low pH soils in Southern China. Open Life Sci 2022; 17:55-63. [PMID: 35284638 PMCID: PMC8860304 DOI: 10.1515/biol-2022-0010] [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: 08/12/2021] [Revised: 11/13/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022] Open
Abstract
Nitrification in agricultural soil is an important process for food production. In acidic soil, nitrification is however also considered to be a major source of N2O production. The nitrification rate largely depends on the community composition of ammonia-oxidizing organisms. To obtain a view of the nitrification rates and N2O emission situations in low pH soils in Southern China and understand their relations with the microbial community composition, here we conducted 15N tracer experiments and microorganism community composition analysis using four acidic agricultural soil samples collected in Southern China. A single dominant community (relative abundance >68%) of the ammonia-oxidizing bacteria and ammonia-oxidizing archaea was observed in the soils with pH = 4.81–6.02. A low amount of NO3–\documentclass[10pt]{article}\usepackage{wasysym}\usepackage[substack]{amsmath}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage[mathscr]{eucal}\usepackage{mathrsfs}\usepackage{pmc}\usepackage[Euler]{upgreek}\pagestyle{empty}\oddsidemargin -1.0in\begin{document}{\text{NO}}_{3}^{\mbox{--}}]\end{document} was produced from the nitrification in the strongly acidic soil (pH = 4.03), and the calculated nitrification rate in this soil was significantly lower than those of other soils with pH = 4.81–6.02. High N2O emissions but low 15N–N2O emissions were observed in the soil with pH = 4.03. Our results suggest that, under aerobic conditions, soil pH is an important factor affecting nitrification through modifying the microorganism composition.
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Affiliation(s)
- Feifei He
- School of Agriculture, Yunnan University , Kunming 650500 , China
| | - Haohao Yu
- School of Agriculture, Yunnan University , Kunming 650500 , China
| | - Dandan Liu
- School of Agriculture, Yunnan University , Kunming 650500 , China
| | - Zheng Li
- School of Agriculture, Yunnan University , Kunming 650500 , China
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Tatsumi C, Azuma WA, Ogawa Y, Komada N. Nitrogen Availability and Microbial Communities of Canopy Soils in a Large Cercidiphyllum japonicum Tree of a Cool-Temperate Old Growth Forest. MICROBIAL ECOLOGY 2021; 82:919-931. [PMID: 33606088 DOI: 10.1007/s00248-021-01707-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Canopy soils on large trees are important for supporting the lives of many canopy plants, and thereby increasing regional biodiversity. However, because of the less accessibility to canopy soils, there is insufficient knowledge on how canopy soils produce available nitrogen (N) for canopy plants through the activity of canopy soil microbes. Canopy soils usually have different soil properties from ground soils, so we hypothesized that canopy soils would have unique microbial communities compared to ground soils, but still provide available N for canopy plants. Here, we compared soil N availability, including net N mineralization and nitrification rate, and microbial communities between canopy soils (organic soils) collected at various heights of a large Cercidiphyllum japonicum tree and ground soils (organic and mineral soils) in a cool-temperate old-growth forest of Japan. The canopy soils had significantly different N availability (mass-based higher but volume-based lower) and microbial communities from the ground mineral soils. Among organic soils, the height of the soil had an impact on the microbial communities but not on the N availability, which agreed with our hypothesis. Despite the decrease in fungal abundance in the higher soils, the increase in certain components of the cellulose-decomposing fungi and oligotrophic bacteria may contribute to the available N production. Also, the abundance of ammonia-oxidizers did not change with the height, which would be important for the nitrification rate. Our study implied canopy soils could provide N to canopy plants partly through the functional redundancy within different microbial communities and constant population of ammonia-oxidizers.
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Affiliation(s)
- Chikae Tatsumi
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Wakana A Azuma
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, 657-8501, Japan.
| | - Yuya Ogawa
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Natsuki Komada
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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20
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Allegrini M, Morales ME, Villamil MB, Zabaloy MC. Ammonia Oxidizing Prokaryotes Respond Differently to Fertilization and Termination Methods in Common Oat's Rhizosphere. Front Microbiol 2021; 12:746524. [PMID: 34690996 PMCID: PMC8527175 DOI: 10.3389/fmicb.2021.746524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Cover crops (CC) have demonstrated beneficial effects on several soil properties yet questions remain regarding their effects on soil microbial communities. Among them, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) have a key role for N cycling in soil and their responses in the rhizosphere of terminated CC deserve further investigation. A greenhouse experiment was established to assess N fertilization (with or without N) and termination methods (glyphosate, mowing, and untreated control) of common oat (Avena sativa L.) as potential drivers of AOA and AOB responses in the rhizosphere. The abundance of amoA genes was determined by quantitative real-time PCR (qPCR), the community structure was assessed with Illumina amplicon sequencing of these genes, while the function was assessed from potential nitrification activity (PNA). While N fertilization had no influence on AOA, the termination method significantly increased amoA gene copies of AOA in mowed plants relative to glyphosate termination or the untreated control (1.76 and 1.49-fold change, respectively), and shifted AOA community structure (PERMANOVA, p<0.05). Ordination methods indicated a separation between AOA communities from control and glyphosate-terminated plants relative to mowed plants for both UniFrac and Aitchison distance. Converserly, N fertilization significantly increased AOB abundance in the rhizosphere of mowed and control plants, yet not in glyphosate-treated plants. Analyses of community structure showed that AOB changed only in response to N fertilization and not to the termination method. In line with these results, significantly higher PNA values were measured in all fertilized samples, regardless of the termination methods. Overall, the results of this study indicated that bacterial and archaeal nitrifiers have contrasting responses to fertlization and plant termination methods. While AOA were responsive to the termination method, AOB were more sensitive to N additions, although, the stimulative effect of N fertilization on amoAAOB abundance was dependent on the termination method.
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Affiliation(s)
- Marco Allegrini
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Marianela E Morales
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Maria B Villamil
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - María Celina Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina.,Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
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21
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Haiming T, Chao L, Kaikai C, Lihong S, Li W, Weiyan L, Xiaoping X, Ke W. Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field. J Appl Microbiol 2021; 132:1307-1318. [PMID: 34487604 DOI: 10.1111/jam.15289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 11/27/2022]
Abstract
AIMS The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5 years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction. METHODS AND RESULTS The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management. CONCLUSIONS The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition. SIGNIFICANCE AND IMPACT OF STUDY The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.
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Affiliation(s)
- Tang Haiming
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Li Chao
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Cheng Kaikai
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Shi Lihong
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Wen Li
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Li Weiyan
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Xiao Xiaoping
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Wang Ke
- Hunan Soil and Fertilizer Institute, Changsha, China
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22
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Wang H, Bagnoud A, Ponce-Toledo RI, Kerou M, Weil M, Schleper C, Urich T. Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils. mSystems 2021; 6:e0054621. [PMID: 34463572 DOI: 10.1128/msystems.00546-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/12/2021] [Indexed: 01/04/2023] Open
Abstract
A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal amoA and 16S rRNA genes to link 16S rRNA gene classification to the novel amoA taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring amoA and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding amoA clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class Nitrososphaeria to seven different AOA (amoA) clades, including two of the most frequently detected clades (Nitrososphaerales γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. IMPORTANCE The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved amoA taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated amoA clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by amoA phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.
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Affiliation(s)
- Haitao Wang
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
| | - Alexandre Bagnoud
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Rafael I Ponce-Toledo
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Melina Kerou
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Micha Weil
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Tim Urich
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
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23
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Buessecker S, Zamora Z, Sarno AF, Finn DR, Hoyt AM, van Haren J, Urquiza Muñoz JD, Cadillo-Quiroz H. Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin. Front Microbiol 2021; 12:659079. [PMID: 34267733 PMCID: PMC8276178 DOI: 10.3389/fmicb.2021.659079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/21/2021] [Indexed: 12/03/2022] Open
Abstract
Tropical peatlands are hotspots of methane (CH4) production but present high variation and emission uncertainties in the Amazon region. This is because the controlling factors of methane production in tropical peats are not yet well documented. Although inhibitory effects of nitrogen oxides (NOx) on methanogenic activity are known from pure culture studies, the role of NOx in the methane cycling of peatlands remains unexplored. Here, we investigated the CH4 content, soil geochemistry and microbial communities along 1-m-soil profiles and assessed the effects of soil NOx and nitrous oxide (N2O) on methanogenic abundance and activity in three peatlands of the Pastaza-Marañón foreland basin. The peatlands were distinct in pH, DOC, nitrate pore water concentrations, C/N ratios of shallow soils, redox potential, and 13C enrichment in dissolved inorganic carbon and CH4 pools, which are primarily contingent on H2-dependent methanogenesis. Molecular 16S rRNA and mcrA gene data revealed diverse and novel methanogens varying across sites. Importantly, we also observed a strong stratification in relative abundances of microbial groups involved in NOx cycling, along with a concordant stratification of methanogens. The higher relative abundance of ammonia-oxidizing archaea (Thaumarchaeota) in acidic oligotrophic peat than ammonia-oxidizing bacteria (Nitrospira) is noteworthy as putative sources of NOx. Experiments testing the interaction of NOx species and methanogenesis found that the latter showed differential sensitivity to nitrite (up to 85% reduction) and N2O (complete inhibition), which would act as an unaccounted CH4 control in these ecosystems. Overall, we present evidence of diverse peatlands likely differently affected by inhibitory effects of nitrogen species on methanogens as another contributor to variable CH4 fluxes.
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Affiliation(s)
- Steffen Buessecker
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Zacary Zamora
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Analissa F Sarno
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Damien Robert Finn
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Alison M Hoyt
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Joost van Haren
- Biosphere 2 Institute, University of Arizona, Oracle, AZ, United States.,Honors College, University of Arizona, Tucson, AZ, United States
| | - Jose D Urquiza Muñoz
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany.,Laboratory of Soil Research, Research Institute of Amazonia's Natural Resources, National University of the Peruvian Amazon, Iquitos, Peru.,School of Forestry, National University of the Peruvian Amazon, Iquitos, Peru
| | - Hinsby Cadillo-Quiroz
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Swette Center for Environmental Biotechnology, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
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24
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Changes in soil ammonia oxidizers and potential nitrification after clear-cutting of boreal forests in China. World J Microbiol Biotechnol 2021; 37:126. [PMID: 34180026 DOI: 10.1007/s11274-021-03087-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
The Korean pine and broad-leaved mixed forests are the most typical and complete ecosystem among the global boreal forests, with extremely important ecological functions. However, few studies on the changes of soil ammonia oxidizers and potential nitrification after clear-cutting of forests are reported. In this study, in contrast to primary Korean pine forests, nitrate (NO3-) was significantly higher in secondary broad-leaved forests, while ammonium (NH4+) was on the contrary. The abundance of ammonia-oxidizing bacteria (AOB) was greatly higher in secondary broad-leaved forests, while levels of ammonia-oxidizing archaea (AOA) were not significantly different between them. The significant differences of community structure of AOA and AOB were observed in different forest types and soil layers. Compared with AOA, community compositions of AOB was more sensitive to forest type. The dominant groups of AOA were Nitrososphaera and Nitrosotalea, and the dominant group of AOB was Nitrosospira, of which Nitrosospira cluster 2 and 4 were functional groups with highly activity. Soil potential nitrification rate (PNR) was higher in secondary broad-leaved forests. Furthermore, PNR and AOB abundance had a significant positive correlation, but no significant correlation with AOA abundance. These results provide insights into the soil nitrogen balance and effects on forest restoration after clear-cutting.
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25
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Yang L, Zhu G, Ju X, Liu R. How nitrification-related N 2O is associated with soil ammonia oxidizers in two contrasting soils in China? THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:143212. [PMID: 33257072 DOI: 10.1016/j.scitotenv.2020.143212] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 06/12/2023]
Abstract
As a key process contributing to N2O emissions, nitrification is regulated by soil microbes and mainly affected by soil pH, NH3 availability, temperature and O2 availability. Current knowledge gaps include how nitrification-related N2O is associated with soil microbes in different pH soils. In the current study, a microcosm incubation experiment was conducted with two contrasting soils of different pH (5.08, 8.30) under controlled conditions. The soils were amended with ammonium sulphate ((NH4)2SO4, 50 mg N kg-1) combined with or without nitrification inhibitors and incubated under 20 °C, 65% water hold capacity (WHC) for three weeks. N2O fluxes, mineral nitrogen (N) concentrations and ammonia oxidizers populations were measured during the incubation to investigate the correlations of nitrification-related N2O with ammonia oxidizers. The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) was used to inhibit nitrification albeit to various inhibition effects with different soils. Acetylene (0.1% v/v C2H2), an inhibitor of AOA and AOB ammonia monooxygenase (AMO), was used to distinguish N2O emissions by nitrifiers and denitrifiers. 1-octyne (5 μM aqueous), a selective specific AOB inhibitor, was used to assess the relative contributions of AOA and AOB to N2O emissions. The results showed that N2O yield for AOA and AOB varied with soil pH. AOB was the key microbial player in alkaline soil, contributing about 85% of nitrification-related N2O. Conversely, about 78% of nitrification-related N2O was contributed by AOA in acidic soil. Furthermore, there was a significant and positive relationship between mineral N (NO2-, NO3-), AOA and AOB populations and nitrification-related N2O in alkaline soil. However, in acidic soil, NO3- concentration and AOA had significantly positive relationships with nitrification-related N2O. To conclude, soil pH was a key factor affecting the contribution of ammonia oxidizers to nitrification-related N2O emissions. AOA-related N2O production dominated at low pH (5.08), while AOB-related N2O was favored in alkaline soil (pH 8.3).
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Affiliation(s)
- Liuqing Yang
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Gaodi Zhu
- College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaotang Ju
- College of Tropical Crops, Hainan University, Haikou 570228, China; Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Rui Liu
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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26
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Peng B, Sun J, Liu J, Xia Z, Dai W. Relative contributions of different substrates to soil N 2O emission and their responses to N addition in a temperate forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144126. [PMID: 33429272 DOI: 10.1016/j.scitotenv.2020.144126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/22/2020] [Accepted: 11/22/2020] [Indexed: 06/12/2023]
Abstract
With increasing nitrogen (N) deposition, soil nitrous oxide (N2O) emission is expected to increase, causing positive feedback to global warming. However, the substrates of soil N2O emission, especially their responses to N addition, are still unclear. Here, we conducted an in situ 15N tracing experiment to study the substrates of N2O (i.e., ammonium-derived, nitrate-derived and organic N-derived N2O emission) under N addition treatment in a temperate forest in northeast China. Nitrate derived N2O through denitrification contributed most to the total N2O emission, pointing to the importance of denitrification under ambient N deposition. NH4NO3 addition of 50 kg N ha-1 yr-1 significantly increased organic N derived N2O on the 6th day after N addition, which suggests that heterotrophic nitrification may be the dominating process with higher N deposition rate. However, because soil pH and the examined functional genes did not change after N addition, future studies should be carried out to understand if the increase of heterotrophic nitrification is transient. Our study emphasizes the role of organic N pool in soil N2O emissions, highlighting the importance of considering the heterotrophic nitrification process while studying soil N cycling or modeling soil N2O emission.
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Affiliation(s)
- Bo Peng
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; College of Life Science and Resources and Environment, Yichun University, Yichun 336000, China.
| | - Jianfei Sun
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation of Nanning Normal University, Nanning, 530001, China.
| | - Jun Liu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Zongwei Xia
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Weiwei Dai
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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27
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Guo H, Gu J, Wang X, Song Z, Nasir M, Tuo X. Elucidating the microbiological characteristics of cyromazine affecting the nitrogen cycle during aerobic composting of pig manure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142812. [PMID: 33071140 DOI: 10.1016/j.scitotenv.2020.142812] [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: 07/18/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Cyromazine as insect growth inhibitor have been frequently detected in the environment, which show a potential threat to environment and soil health. Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet. In this study, quantitative polymerase chain reaction (qPCR) and sequencing of nitrifying and denitrifying bacteria were conducted to investigate the dynamic effects of cyromazine on nitrogen conversion during laboratory-based composting. Results showed that the presence of cyromazine significantly reduced the abundance of amoA gene during the thermophilic phase of composting (p < 0.01), resulting in lower oxidation of NH4+-N. The archaea amoA gene was more resistant to cyromazine. The nirK gene was more abundant than the nirS gene during composting and was significantly reduced only under high concentrations of cyromazine (p < 0.01). The high dose of cyromazine (15 mg/kg) severely damaged the nitrogen fixation capacity of compost products. Cyromazine exhibited an inhibition effect on richness (ACE, Chao) of nitrifying and denitrifying microorganisms during the thermophilic period, while increased the diversity (shannon) at all stages of composting. Pseudomonas_formosensis was the core denitrifiers that harbored nosZ gene, Nitrosomonas_eutropha and Nitrosospira_sp_Nl5 were the dominant nitrifier that harbored amoA gene, and these species have a negative response to cyromazine. Network analysis indicated that the dominant bacteria harboring amoA and nosZ genes were hubs of nitrogen oxidation and reduction processes. Structural equation modeling revealed that NO2--N conversion played a crucial role in driving denitrification, and increase of NH4+-N content was attributed to the inhibition of nitrification and denitrification during composting caused by cyromazine.
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Affiliation(s)
- Honghong Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mubasher Nasir
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaxia Tuo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
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28
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Bacterial and Archaeal Structural Diversity in Several Biodeterioration Patterns on the Limestone Walls of the Old Cathedral of Coimbra. Microorganisms 2021; 9:microorganisms9040709. [PMID: 33808176 PMCID: PMC8065406 DOI: 10.3390/microorganisms9040709] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 11/25/2022] Open
Abstract
The “University of Coimbra-Alta and Sofia” area was awarded the UNESCO World Heritage Site distinction in 2013. The Old Cathedral of Coimbra, a 12th-century limestone monument located in this area, has been significantly impacted during the last 800 years by physical, chemical, and biological processes. This led to the significant deterioration of some of its structures and carvings, with loss of aesthetical, cultural, and historical values. For this work, deteriorated spots of the walls of three semi-open chapels from the cloister of the Cathedral were sampled to ascertain their bacterial and archaeal structural diversity. Based on Next-Generation Sequencing (NGS) result analysis, we report the presence of microbial populations that are well adapted to an ecosystem with harsh conditions and that can establish a diverse biofilm in most cases. While it was possible to determine dominant phylogenetic groups in Archaea and Bacteria domains, there was no clear connection between specific core microbiomes and the different deterioration patterns analyzed. The distribution of these archaeal and bacterial communities within the analyzed biodeterioration spots suggests they are more influenced by abiotic factors (i.e., water availability, salinity, etc.), although they influence (and are influenced by) the algal and fungal population composition in this ecosystem. This work provides valuable information that can assist in establishing future guidelines for the preservation and conservation of this kind of historic stone monuments.
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29
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Nardi P, Laanbroek HJ, Nicol GW, Renella G, Cardinale M, Pietramellara G, Weckwerth W, Trinchera A, Ghatak A, Nannipieri P. Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications. FEMS Microbiol Rev 2021; 44:874-908. [PMID: 32785584 DOI: 10.1093/femsre/fuaa037] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.
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Affiliation(s)
- Pierfrancesco Nardi
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - Giancarlo Renella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Centro Ecotekne - via Provinciale Lecce-Monteroni, I-73100, Lecce, Italy
| | - Giacomo Pietramellara
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Alessandra Trinchera
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Paolo Nannipieri
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
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Liu J, Liu W, Zhang Y, Chen C, Wu W, Zhang TC. Microbial communities in rare earth mining soil after in-situ leaching mining. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142521. [PMID: 33035989 DOI: 10.1016/j.scitotenv.2020.142521] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/19/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.
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Affiliation(s)
- Jingjing Liu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, China.
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University, Baoding, China
| | - Yingbin Zhang
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, China
| | - Chongjun Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, China
| | - Tian C Zhang
- Department of Civil & Environmental Engineering, University of Nebraska-Lincoln, Omaha, USA
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31
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Wang C, Wu R, Song Y, Guo J, Liu R, Cui Y. Differences in nitrification and ammonium-oxidising prokaryotes in the process of wetland restoration. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 56:136-144. [PMID: 33259261 DOI: 10.1080/10934529.2020.1852845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) are ammonium oxidising prokaryotes that can drive soil nitrification in wetlands. During the restoration of wetlands, different types of land use soils (agricultural soil [AS], restored wetland soil [RS], and natural wetland soil [NWS]) are present. However, studies on the effects of changes in the types of land use in wetlands during restoration on nitrification and the community composition of AOA and AOB are still not well understood. In this study, the differences in the potential nitrification rate (PNR) and community composition of AOA and AOB in AS, RS, and NWS were compared and discussed. The results indicated that the PNRs in the AS, RS, and NWS were on the same order of magnitude. Nitrification was mainly driven by AOB. High-throughput sequencing results showed that the genus Nitrososphaera of AOA and unclassified_o_Nitrosomonadales of AOB were only detected in the AS. Redundancy analysis (RDA) results indicated that the community composition of AOA was mostly influenced by pH, while TC was the most influential variable on the community composition of AOB. Our study provides a basis for distinguishing the roles of ammonium-oxidising prokaryotes in nitrification and further understanding the changes in nitrifying activity in wetlands during restoration.
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Affiliation(s)
- Chunyong Wang
- School of Chemical and Environmental Engineering, Liaoning University of Technology, Jinzhou, PR China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Rui Wu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yi Song
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Jianbo Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yanshan Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
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Liang D, Ouyang Y, Tiemann L, Robertson GP. Niche Differentiation of Bacterial Versus Archaeal Soil Nitrifiers Induced by Ammonium Inhibition Along a Management Gradient. Front Microbiol 2020; 11:568588. [PMID: 33281763 PMCID: PMC7689314 DOI: 10.3389/fmicb.2020.568588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/12/2020] [Indexed: 01/08/2023] Open
Abstract
Soil nitrification, mediated mainly by ammonia oxidizing archaea (AOA) and bacteria (AOB), converts ammonium (NH4+) to nitrite (NO2−) and thence nitrate (NO3−). To better understand ecological differences between AOA and AOB, we investigated the nitrification kinetics of AOA and AOB under eight replicated cropped and unmanaged ecosystems (including two fertilized natural systems) along a long-term management intensity gradient in the upper U.S. Midwest. For five of eight ecosystems, AOB but not AOA exhibited Haldane kinetics (inhibited by high NH4+ additions), especially in perennial and successional systems. In contrast, AOA predominantly exhibited Michaelis-Menten kinetics, suggesting greater resistance to high nitrogen inputs than AOB. These responses suggest the potential for NH4+-induced niche differentiation between AOA and AOB. Additionally, long-term fertilization significantly enhanced maximum nitrification rates (Vmax) in the early successional systems for both AOA and AOB, but not in the deciduous forest systems. This was likely due to pH suppression of nitrification in the acidic forest soils, corroborated by a positive correlation of Vmax with soil pH but not with amoA gene abundance. Results also demonstrated that soil nitrification potentials were relatively stable, as there were no seasonal differences. Overall, results suggest that (1) NH4+ inhibition of AOB but not AOA could be another factor contributing to niche differentiation between AOA and AOB in soil, and (2) nitrification by both AOA and AOB can be significantly promoted by long-term nitrogen inputs.
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Affiliation(s)
- Di Liang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States.,W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
| | - Yang Ouyang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - Lisa Tiemann
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - G Philip Robertson
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States.,W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
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Xia WW, Zhao J, Zheng Y, Zhang HM, Zhang JB, Chen RR, Lin XG, Jia ZJ. Active Soil Nitrifying Communities Revealed by In Situ Transcriptomics and Microcosm-Based Stable-Isotope Probing. Appl Environ Microbiol 2020; 86:e01807-20. [PMID: 32978127 PMCID: PMC7657639 DOI: 10.1128/aem.01807-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/17/2020] [Indexed: 01/19/2023] Open
Abstract
Long-term nitrogen field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes in communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to those of 13C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimens for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N-fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable-isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and Nitrosospira viennensis-like AOA, despite the strong advantage of AOB over AOA in the N-fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was the opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidence that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in 13C-labeled microcosms.IMPORTANCE The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results for active AOA and AOB, although an apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that the soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosms can serve as powerful tools to test the theory of environmental filtering on the key functional microbial guilds.
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Affiliation(s)
- Wei-Wei Xia
- Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yan Zheng
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
| | - Hui-Min Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jia-Bao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Rui-Rui Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xian-Gui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhong-Jun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Lu B, Qian J, Wang P, Wang C, Hu J, Li K, He X, Jin W. Effect of perfluorooctanesulfonate (PFOS) on the rhizosphere soil nitrogen cycling of two riparian plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140494. [PMID: 32886976 DOI: 10.1016/j.scitotenv.2020.140494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Here, we examined the effects of low and high concentrations of perfluorooctanesulfonate (PFOS) on rhizosphere soil N cycling processes in the presence of Lythrum salicaria and Phragmites communis over 4 months. Compared with the control group, the nitrate nitrogen (NO3--N) content of the bulk soil in the low PFOS (0.1 mg kg-1) treatment significantly decreased (27.7%), the ammonium nitrogen (NH4+-N) content significantly increased (8.7%), and the pH value and total organic carbon (TOC) content slightly increased (0.3% and 1.1%, respectively). Compared with the low PFOS treatment, the content of NO3-N, NH4+-N and pH value in the bulk soil of the high PFOS treatment (50 mg kg-1) significantly increased (1.0%, 53.8% and 61.8%, respectively), and the TOC content significantly decreased (8.2%). Soil protease levels were high in the low PFOS treatment, but low in the high PFOS treatment. PFOS produced inverted U-shaped responses in the potential nitrification (1.5, 3.0, and 1.1 mg N d-1 kg-1 in no, low, and high PFOS, respectively), denitrification (0.19, 0.30, and 0.22 mg N d-1 kg-1 in no, low, and high PFOS, respectively), and N2O emission rates (0.01, 0.03, and 0.02 mg N d-1 kg-1 in no, low, and high PFOS, respectively) of bulk soil. The abundance of the archaea amoA gene decreased with increasing PFOS concentration, whereas that of bacterial amoA increased; inverted U-shaped responses were observed for narG, nirK, nirS, and nosZ. In the PFOS-contaminated rhizosphere soil, the observed changes differed from those in the bulk soil and differed between treatments. P. communis tended to upregulate each step of the nitrogen cycle under low PFOS conditions, whereas L. salicaria tended to inhibit them. Under high PFOS conditions, both test plants tended to act as inhibitors of the soil N-cycle; thus, the effects of PFOS on soil N transformation were plant-specific.
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Affiliation(s)
- Bianhe Lu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Jin Qian
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Jing Hu
- Wetland Biogeochemistry Laboratory, Soil and Water Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL, USA
| | - Kun Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Xixian He
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Wen Jin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
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Xie F, Zhang G, Zheng Q, Liu K, Yin X, Sun X, Saud S, Shi Z, Yuan R, Deng W, Zhang L, Cui G, Chen Y. Beneficial Effects of Mixing Kentucky Bluegrass With Red Fescue via Plant-Soil Interactions in Black Soil of Northeast China. Front Microbiol 2020; 11:556118. [PMID: 33193137 PMCID: PMC7656059 DOI: 10.3389/fmicb.2020.556118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Continuous monoculture of cool-season turfgrass causes soil degradation, and visual turf quality decline is a major concern in black soil regions of Northeast China. Turf mixtures can enhance turfgrass resistance to biotic and abiotic stresses and increase soil microbial diversity. Understanding mechanism by plant-soil interactions and changes of black soil microbial communities in turf mixture is beneficial to restoring the degradation of urbanized black soils and maintaining sustainable development of urban landscape ecology. In this study, based on the previous research of different sowing models, two schemes of turf monoculture and mixture were conducted in field plots during 2016-2018 in a black soil of Heilongjiang province of Northeast China. The mixture turf was established by mixing 50% Kentucky bluegrass "Midnight" (Poa pratensis L.) with 50% Red fescue "Frigg" (Festuca rubra L.); and the monoculture turf was established by sowing with pure Kentucky bluegrass. Turf performance, soil physiochemical properties, and microbial composition from rhizosphere were investigated. Soil microbial communities and abundance were analyzed by Illumina MiSeq sequencing and quantitative PCR methods. Results showed that turfgrass quality, turfgrass biomass, soil organic matter (SOM), urease, alkaline phosphatase, invertase, and catalase activities increased in PF mixture, but disease percentage and soil pH decreased. The microbial diversity was also significantly enhanced under turf mixture model. The microbial community compositions were significantly different between the two schemes. Turf mixtures obviously increased the abundances of Beauveria, Lysobacter, Chryseolinea, and Gemmatimonas spp., while remarkably reduced the abundances of Myrothecium and Epicoccum spp. Redundancy analysis showed that the compositions of bacteria and fungi were related to edaphic parameters, such as SOM, pH, and enzyme activities. Since the increasing of turf quality, biomass, and disease resistance were highly correlated with the changes of soil physiochemical parameters and microbial communities in turf mixture, which suggested that turf mixture with two species (i.e., Kentucky blue grass and Red fescue) changed soil microbial communities and enhanced visual turfgrass qualities through positive plant-soil interactions by soil biota.
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Affiliation(s)
- Fuchun Xie
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Gaoyun Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Qianjiao Zheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Kemeng Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China.,Beijing Oriental Garden Environment Co., Ltd, Beijing, China
| | - Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xiaoyang Sun
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Shah Saud
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Zhenjie Shi
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Runli Yuan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Wenjing Deng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Lu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yajun Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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36
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Effects of Zeolite and Biochar Addition on Ammonia-Oxidizing Bacteria and Ammonia-Oxidizing Archaea Communities during Agricultural Waste Composting. SUSTAINABILITY 2020. [DOI: 10.3390/su12166336] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The effects of zeolite and biochar addition on ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities during agricultural waste composting were determined in this study. Four treatments were conducted as follows: Treatment A as the control with no additive, Treatment B with 5% of zeolite, Treatment C with 5% of biochar, and Treatment D with 5% of zeolite and 5% biochar, respectively. The AOB and AOA amoA gene abundance as well as the ammonia monooxygenase (AMO) activity were estimated by quantitative PCR and enzyme-linked immunosorbent assay, respectively. The relationship between gene abundance and AMO enzyme activity was determined by regression analysis. Results indicated that the AOB was more abundant than that of AOA throughout the composting process. Addition of biochar and its integrated application with zeolite promoted the AOB community abundance and AMO enzyme activity. Significant positive relationships were obtained between AMO enzyme activity and AOB community abundance (r2 = 0.792; P < 0.01) and AOA community abundance (r2 = 0.772; P < 0.01), indicating that both bacteria and archaea played significant roles in microbial ammonia oxidation during composting. Using biochar and zeolite might promote the nitrification activity by altering the sample properties during agricultural waste composting.
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37
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Wang Y, Shen L, Wu J, Zhong F, Cheng S. Step-feeding ratios affect nitrogen removal and related microbial communities in multi-stage vertical flow constructed wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 721:137689. [PMID: 32169643 DOI: 10.1016/j.scitotenv.2020.137689] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/25/2020] [Accepted: 03/01/2020] [Indexed: 06/10/2023]
Abstract
Step-feeding (SF) strategies have been adopted in several types of constructed wetlands (CWs) to enhance nitrogen (N) removal. However, it is unclear how SF affects the N-transforming bacterial communities in CWs. Herein, four multi-stage vertical flow constructed wetlands (MS-VFCWs), each including three vertical flow stages (stage 1-3), were operated under different SF ratios (0%, 10%, 20% and 30%) in the stage 2. The physicochemical influent and effluent parameters, i.e., redox potential (ORP), pH value, chemical oxygen demand (COD), total nitrogen (TN), ammonia (NH4+-N), nitrate (NO3--N), and nitrite (NO2--N), free-ammonia (FA) concentration, COD/TN ratio, as well as the abundance, structure, and activity of N-transforming bacteria were investigated. Results showed that N removal in a multi-stage vertical flow constructed wetland in the absence of SF was 45.0 ± 7.74%. Alternatively, a combined SF ratio of 20% increased N removal to 61.7% ± 4.50%, accounting for a 37.1% increase compared to the SF ratio of 0%. In the microbial community, FA was determined to be the primary physicochemical parameter governing nitrification processes in MS-VFCWs. Further, partial nitrification processes played an important role in ammonium removal during stage 1, while ammonia-oxidizing archaea were major contributors to ammonium removal in stage 3. Furthermore, abundance of nitrite reductase genes (nirS, nirK) and relative abundance of denitrifying bacteria increased with increasing SF ratio; while the nirS/nirK ratio and the alpha diversity of nirK denitrifiers were significantly affected by SF ratios, and the influent NO3--N concentration was related to a shift in denitrifier composition toward strains containing the nirS gene. Autotrophic (e.g., Thiobacillus, Sulfurimonas, Arenimonas, Gallionella and Methyloparacoccus) and facultative chemolithoautotrophic (e.g., Pseudomonas and Denitratisoma) denitrifying bacteria were enriched in stage 2. Hence, the synergy between heterotrophic and autotrophic denitrifying bacteria promoted excellent N removal efficiency with a low COD/TN ratio.
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Affiliation(s)
- Ying Wang
- Tongji University, College of Environmental Science and Engineering, Key Laboratory of Yangtze River Water Environment, Ministry of Education, 200092, PR China
| | - Linya Shen
- Tongji University, College of Environmental Science and Engineering, Key Laboratory of Yangtze River Water Environment, Ministry of Education, 200092, PR China
| | - Juan Wu
- Tongji University, College of Environmental Science and Engineering, Key Laboratory of Yangtze River Water Environment, Ministry of Education, 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China; Shanghai Engineering Research Center of Landscape Water Environment, Shanghai 200031, PR China.
| | - Fei Zhong
- Nantong University, School of Life Science, Nantong 226019, PR China
| | - Shuiping Cheng
- Tongji University, College of Environmental Science and Engineering, Key Laboratory of Yangtze River Water Environment, Ministry of Education, 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China; Shanghai Engineering Research Center of Landscape Water Environment, Shanghai 200031, PR China.
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Yang X, Ni K, Shi Y, Yi X, Ji L, Ma L, Ruan J. Heavy nitrogen application increases soil nitrification through ammonia-oxidizing bacteria rather than archaea in acidic tea (Camellia sinensis L.) plantation soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137248. [PMID: 32084690 DOI: 10.1016/j.scitotenv.2020.137248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/09/2020] [Accepted: 02/09/2020] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) fertilizer is widely used in agricultural ecosystems and influences N transformation processes in the soil such as nitrification. However, whether nitrification is primarily dominated by ammonia-oxidizing bacteria (AOB) or archaea (AOA) under heavy N application is still under debate. In the present work, the effect of long-term (12 years) N fertilization on soil nitrification and the key influencing factors were investigated in acidic tea plantation soil that received four different rates of N application (0, 119, 285, and 569 kg N ha-1 yr-1). Nitrification potential was measured and partitioned using chemical inhibitors. The abundance of functional genes involved in ammonia oxidation was quantified using quantitative polymerase chain reaction (qPCR). Ammonia-oxidizing communities were identified by shotgun metagenome sequencing. Potential nitrification rate in tea plantation soil was mainly dominated by autotrophic nitrification (PNRA) (71-79%). PNRA and heterotrophic nitrification (PNRH) were both significantly increased by heavy N (569 kg ha-1) application. Moreover, PNRA was mainly due to the contribution of AOB (52-66%) in N-treated soils, and N569 significantly increased the AOB contribution without affecting the AOA contribution. N569 increased the functional gene abundance of AOB and TAO100 (a non-halophilic γ-AOB) but decreased that of AOA. The dominant AOB (Nitrosomonas, Nitrosospira, and Nitrosococcus), AOA (Nitrososphaera and Nitrosopumilus) and commamox (Nitrospira) groups were profoundly altered by long-term N application rates. Partial least squares regression showed that total nitrification (PNRT), PNRA, and PNRAOB were primarily explained by the functional gene abundance of nitrifiers whereas PNRH and PNRAOA were closely associated with soil and pruned litter properties. Moreover, structural equation modeling (SEM) revealed that long-term N application significantly and indirectly affected nitrification potential by directly influencing soil properties, pruned litter properties, and functional gene abundance. Understanding the relative contribution of AOA and AOB to nitrification may help to better regulate N fertilizer use in agricultural ecosystems.
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Affiliation(s)
- Xiangde Yang
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China
| | - Kang Ni
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Yuanzhi Shi
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Xioayun Yi
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Lingfei Ji
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Lifeng Ma
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Jianyun Ruan
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
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Ding LJ, Cui HL, Nie SA, Long XE, Duan GL, Zhu YG. Microbiomes inhabiting rice roots and rhizosphere. FEMS Microbiol Ecol 2020; 95:5420819. [PMID: 30916760 DOI: 10.1093/femsec/fiz040] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/26/2019] [Indexed: 11/12/2022] Open
Abstract
Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.
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Affiliation(s)
- Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hui-Ling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - San-An Nie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Xi-En Long
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
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40
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Wen D, Valencia A, Ordonez D, Chang NB, Wanielista M. Comparative nitrogen removal via microbial ecology between soil and green sorption media in a rapid infiltration basin for co-disposal of stormwater and wastewater. ENVIRONMENTAL RESEARCH 2020; 184:109338. [PMID: 32172072 DOI: 10.1016/j.envres.2020.109338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/16/2020] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
In this study, a rapid infiltration basin (RIB) designed as green infrastructure for co-disposal of wastewater effluent and stormwater runoff was retrofitted for sustainable groundwater recharge after nitrogen removal. For comparison of nitrogen removal efficiency via different filtration media, the RIB was divided into two sub-basins for different filtration processes. One sub-basin was filled with a native sandy soil with about 2-4% clay (Control RIB), and the other sub-basin was modified with Biosorption Activated Media (BAM) (BAM RIB), for the enhancement of microbial nitrogen removal. The two sub-basins accept an equal amount of excess reclaimed wastewater in non-storm periods, and stormwater during periodic storm events. The infiltrate in both the BAM RIB and the Control RIB eventually reaches the Upper Floridan Aquifer. The seven microbial species involved in this microbial ecology study are nitrite oxidizing bacteria (NOB), ammonia oxidizing bacteria (AOB), anaerobic oxidation of ammonium (anammox) bacteria, complete ammonia oxidizer (Comammox) bacteria, denitrifiers, dissimilatory nitrate reduction to ammonium (DNRA) and ammonia-oxidizing archaea (AOA). The population dynamics study was conducted with the aid of the quantitative polymerase chain reaction (qPCR) for the quantification of the microbial gene population in support of microbial ecology discovery. The qPCR results demonstrated the competition effect between AOA, AOB, and Comammox, the inhibition effect between NOB and DNRA with the presence of anammox, and the complementary effect due to an abundance of NOB and AOB in the microbial ecology. Although, competition between denitrifiers and DNRA was expected to impact population dynamics, both microbial species were found to be the most predominant in both control and BAM RIBs. Research findings indicate that the use of BAM RIB achieves significantly efficient nitrogen removal driven by complementary effects in the microbial ecology.
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Affiliation(s)
- Dan Wen
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Andrea Valencia
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Diana Ordonez
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Ni-Bin Chang
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA.
| | - Martin Wanielista
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
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Guo Y, Rene ER, Wang J, Ma W. Biodegradation of polyaromatic hydrocarbons and the influence of environmental factors during the co-composting of sewage sludge and green forest waste. BIORESOURCE TECHNOLOGY 2020; 297:122434. [PMID: 31787509 DOI: 10.1016/j.biortech.2019.122434] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
The main aim of this research was to study the biodegradation of polycyclic aromatic hydrocarbons (PAHs) and the influence of environmental factors during composting in order to realize the utilization of PAHs contaminated sewage sludge. A production scale compost experiment was conducted with three mixtures of sewage sludge (SS): green forest waste (GFW) at quality ratios of 3:1 (T1), 3:2 (T2) and 3:3 (T3). The residual concentration of PAHs in the three treatments met the permissible limit prescribed by the Agricultural Sludge Pollutant Control Standard (GB 4284-2018). The biodegradation rates of PAHs were 0.0280, 0.0281 and 0.0218 mg/d, and removal efficiencies were 70.7%, 75.2% and 62.4% in T1, T2, T3, respectively, which followed the first-order rate kinetics. The residual concentration of PAHs in T2 was the lowest (1.81 mg/kg), while the germination index (GI) of Tall Fescues (~0.9) was the highest during 50 days of co-composting. The bacterial diversity negatively correlated with the residual PAHs content. The main genus, Bacillus, Pseudomonas and Methylotenera, with cellulose-degrading and PAHs co-metabolizing functions contributed significantly to sludge maturation and PAHs degradation. The dominant microorganisms, Pseudomonas, Sphingobacterium and Chitinophagaceae_uncultured, could support the high removal rate of PAHs in T2. Temperature, pH, total organic carbon (TOC), total nitrogen (TN) and carbon/nitrogen (C/N) ratio had significant positive effect on the compost maturity and quality, and these parameters correlated with the PAHs biodegradation efficiency during composting, especially in T2.
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Affiliation(s)
- Yating Guo
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Eldon R Rene
- IHE-Delft, Institute for Water Education, Department of Environmental Engineering and Water Technology, Westvest 7, 2611AX Delft, the Netherlands
| | - Junjing Wang
- Beijing Drainage Group Technology Research and Development Center, Beijing 100124, China
| | - Weifang Ma
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
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Ammonia- and Methane-Oxidizing Bacteria: The Abundance, Niches and Compositional Differences for Diverse Soil Layers in Three Flooded Paddy Fields. SUSTAINABILITY 2020. [DOI: 10.3390/su12030953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ammonia oxidizing bacteria (AOB), Ammonia oxidizing archaea (AOA) and methane oxidizing bacteria (MOB) play cogent roles in oxidation and nitrification processes, and hence have important ecological functions in several ecosystems. However, their distribution and compositional differences in different long-term flooded paddy fields (FPFs) management at different soil depths remains under-investigated. Using qPCR and phylogenetic analysis, this study investigated the abundance, niches, and compositional differences of AOA, AOB, and MOB along with their potential nitrification and oxidation rate in three soil layers from three FPFs (ShaPingBa (SPB), HeChuan (HC), and JiDi (JD)) in Chongqing, China. In all the FPFs, CH4 oxidation occurred mainly in the surface (0–3 cm) and subsurface layers (3–5 cm). A significant difference in potential methane oxidation and nitrification rates was observed among the three FPFs, in which SPB had the highest. The higher amoA genes are the marker for abundance of AOA compared to AOB while pmoA genes, which is the marker for MOB abundance and diversity, indicated their significant role in the nitrification process across the three FPFs. The phylogenetic analysis revealed that AOA were mainly composed of Nitrososphaera, Nitrosospumilus, and Nitrosotalea, while the genus Nitrosomonas accounted for the greatest proportion of AOB in the three soil layers. MOB were mainly composed of Methylocaldum and Methylocystis genera. Overall, this finding pointed to niche differences as well as suitability of the surface and subsurface soil environments for the co-occurrence of ammonia oxidation and methane oxidation in FPFs.
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Laffite A, Florio A, Andrianarisoa KS, Creuze des Chatelliers C, Schloter‐Hai B, Ndaw SM, Periot C, Schloter M, Zeller B, Poly F, Le Roux X. Biological inhibition of soil nitrification by forest tree species affectsNitrobacterpopulations. Environ Microbiol 2020; 22:1141-1153. [DOI: 10.1111/1462-2920.14905] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/25/2019] [Accepted: 12/18/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Amandine Laffite
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Alessandro Florio
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | | | - Charline Creuze des Chatelliers
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Brigitte Schloter‐Hai
- Research Unit for Comparative Microbiome AnalysisHelmholtz Zentrum München D‐85764 Ingolstädter Landstraße 1 Neuherberg Germany
| | - Sidy M. Ndaw
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Charlotte Periot
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Michael Schloter
- Research Unit for Comparative Microbiome AnalysisHelmholtz Zentrum München D‐85764 Ingolstädter Landstraße 1 Neuherberg Germany
| | - Bernd Zeller
- Biogéochimie des Ecosystèmes ForestiersINRA Grand‐EST Nancy UR 1138 Route d'Amance, 54280 Champenoux France
| | - Franck Poly
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
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Zhang X, Duan P, Wu Z, Xiong Z. Aged biochar stimulated ammonia-oxidizing archaea and bacteria-derived N 2O and NO production in an acidic vegetable soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 687:433-440. [PMID: 31212151 DOI: 10.1016/j.scitotenv.2019.06.128] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 06/09/2023]
Abstract
Both nitrous oxide (N2O) and nitric oxide (NO) emissions are typically high in greenhouse-based high N input vegetable soils. Biochar amendment has been widely recommended for mitigating soil N2O emissions in agriculture. However, knowledge of the regulatory mechanisms of fresh and aged biochar for both N2O and NO production during ammonia oxidation is lacking. Two vegetable soils with different pH values were used in aerobic incubation experiments with 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), 1-octyne and acetylene. The relative importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to N2O and NO production was investigated as influenced by fresh and aged biochar amendments. The results showed that AOA dominated N2O production in acidic soil, while AOB dominated N2O production in alkaline soil. Aged biochar stimulated both AOA- and AOB-derived N2O and NO production by 84.8 and 340%, respectively, in acidic soil but only increased AOA-derived N2O and NO production in alkaline soil. Fresh biochar amendment increased AOA- and AOB-derived NO in acidic soil and AOA-derived NO in alkaline soil but had negligible effects on AOA- and AOB-derived N2O in both soils. Fresh biochar decreased AOA-amoA but increased AOB-amoA gene abundances in acidic soil, whereas aged biochar increased AOA- and AOB-amoA gene abundances in both soils. These findings improved our understanding of N2O and NO production mechanisms under different biochar amendments in alkaline and acidic vegetable soils.
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Affiliation(s)
- Xi Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengpeng Duan
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Wu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Norton J, Ouyang Y. Controls and Adaptive Management of Nitrification in Agricultural Soils. Front Microbiol 2019; 10:1931. [PMID: 31543867 PMCID: PMC6728921 DOI: 10.3389/fmicb.2019.01931] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.
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Affiliation(s)
- Jeanette Norton
- Department of Plants, Soils and Climate, Utah State University, Logan, UT, United States
| | - Yang Ouyang
- Department of Microbiology and Plant Biology, Institute of Environmental Genomics, University of Oklahoma, Norman, OK, United States
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Wang L, Xia X, Zhang W, Wang J, Zhu L, Wang J, Wei Z, Ahmad Z. Separate and joint eco-toxicological effects of sulfadimidine and copper on soil microbial biomasses and ammoxidation microorganisms abundances. CHEMOSPHERE 2019; 228:556-564. [PMID: 31055070 DOI: 10.1016/j.chemosphere.2019.04.165] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
Heavy metals and antibiotics residues in agricultural soils are attracting more and more attention. A laboratory study was conducted to evaluate the single and combined effects of sulfadimidine (SM2) (0.05, 0.20, 0.80 mmol/kg) and copper (Cu) (1.60 mmol/kg) on soil microbial biomasses and ammoxidation microorganisms abundances after 7, 14, 21 and 28 days. The results demonstrated that the single and combined contaminations had a significant and persistent inhibitory effect on soil bacteria, fungi and actinomycetes populations and amoA gene copies of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) (Except SM2 0.05 and 0.20 mmol/kg on 7 and 14 d and SM2 0.05 mmol/kg on 21 d led to a stimulatory effect on fungi and AOA-amoA gene, respectively). With higher dosage and longer exposure time, the toxic effect of single and combined contaminants on soil bacteria, fungi and actinomycetes as well as on the amoA gene of AOA and AOB was greatly reinforced. Combined contaminants produced more toxicity than the chemicals were used alone. Overall, the interaction effects of SM2 and Cu on bacteria (on 14, 21 and 28 d), fungi and AOA-amoA were mainly synergism, in contrast, on actinomycetes (on 14, 21 and 28 d) and AOB-amoA were mainly antagonism. The order of the toxic effects of the single Cu and combined contaminants on microbial activity was: bacteria > actinomycetes > fungi. Furthermore, AOB-amoA was more sensitive to both contaminants toxicity than AOA-amoA, while AOA-amoA gene copies were greater than AOB-amoA gene copies about one order of magnitude.
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Affiliation(s)
- Lanjun Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Xiaoming Xia
- College of Plant Protection, Shandong Agricultural University, Taian, 271018, China.
| | - Wenjie Zhang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Jinhua Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Lusheng Zhu
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Jun Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Ziyan Wei
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Zulfiqar Ahmad
- Department of Environmental Sciences, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan.
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Nguyen LTT, Broughton K, Osanai Y, Anderson IC, Bange MP, Tissue DT, Singh BK. Effects of elevated temperature and elevated CO 2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:81-89. [PMID: 31026646 DOI: 10.1016/j.scitotenv.2019.04.181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Rising global air temperature and atmospheric CO2 are expected to have considerable effects on soil nutrient cycling and plant productivity. Soil nitrification controlled by ammonia-oxidizing bacteria and archaea (AOB and AOA) communities plays a key role in contributing to plant nitrogen (N) availability; however, response of soil nitrification and functional microbial communities to climate change and subsequent consequences for crop yields remain largely unknown. Cotton productivity is a function of temperature and N availability under well-watered conditions. In general, cotton growth responds positively to elevated CO2, but simultaneous warming may offset benefits of rising CO2. In this study, cotton was used as a model system to elucidate the short-term response of soil nitrification and ammonia-oxidizing communities to elevated temperature and elevated CO2 using field-based environmentally-controlled chambers. Elevated temperature (ambient + 1.1 °C) altered the AOA community, while elevated temperature and elevated CO2 (ambient + 132 ppm) significantly increased soil nitrification rate and shifted AOB and AOA communities, but these effects depended on cotton developmental stages. Ammonia-oxidizing community abundance and structure were statistically correlated with nitrifying activity. Our findings suggest that climate change will positively affect soil nitrifying communities, leading to an increase in process rates and subsequent N availability, which is directly linked to crop productivity.
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Affiliation(s)
- Linh T T Nguyen
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Katie Broughton
- CSIRO Agriculture and Food, Australian Cotton Research Institute, Locked Bag 59, Narrabri, NSW 2390, Australia
| | - Yui Osanai
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Michael P Bange
- CSIRO Agriculture and Food, Australian Cotton Research Institute, Locked Bag 59, Narrabri, NSW 2390, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia; Global Centre for Land-Based Innovation, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
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48
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Zhou S, Zhang X, Liao X, Wu Y, Mi J, Wang Y. Effect of Different Proportions of Three Microbial Agents on Ammonia Mitigation during the Composting of Layer Manure. Molecules 2019; 24:molecules24132513. [PMID: 31324049 PMCID: PMC6651566 DOI: 10.3390/molecules24132513] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/18/2019] [Accepted: 07/03/2019] [Indexed: 01/22/2023] Open
Abstract
Odor emissions represent one of the important issues of aerobic composting. The addition of microbial agents to compost is an important method for solving this problem, but this process is often unstable when a single microbial agent is added to the compost. Therefore, in this study, five treatments comprising different proportions of Bacillus stearothermophilus, Candida utilis, and Bacillus subtilis were tested to determine the best combination of the three microbial agents for ammonia reduction, as follows: control group (CK), 2:1:1 (A), 1:1:2 (B), 1:2:1 (C), and 1:1:1 (D). Compared with the CK group, the A, B, C, and D groups reduced ammonia emissions by 17.02, 9.68, 53.11, and 46.23%, respectively. The total ammonia emissions were significantly lower in C and D than in CK (p < 0.05). These two treatment groups had significantly increased nitrate nitrogen concentrations and decreased pH values and ammonium nitrogen concentrations (p < 0.05). Throughout the composting process, the total bacterial number was significantly higher in C and D than in CK (p < 0.05). Therefore, it is likely that B. stearothermophilus, C. utilis, and B. subtilis compounded from 1:2:1 (C) to 1:1:1 (D) reduced the ammonia emissions due to (1) a reduction in the pH and (2) the promotion of the growth of ammonia-oxidizing bacteria and the conversion of ammonium nitrogen to nitrate nitrogen. This study provides a theoretical basis and technical support for the odor problem of layer manure compost and promotes the development of composting technology.
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Affiliation(s)
- Shizheng Zhou
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
| | - Xinyi Zhang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
| | - Xindi Liao
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key lab of Chicken Genetics, Breeding and reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Yinbao Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key lab of Chicken Genetics, Breeding and reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Jiandui Mi
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key lab of Chicken Genetics, Breeding and reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Yan Wang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key lab of Chicken Genetics, Breeding and reproduction, Ministry of Agriculture, Guangzhou 510642, China.
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Sun X, Zhong T, Zhang L, Zhang K, Wu W. Reducing ammonia volatilization from paddy field with rice straw derived biochar. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:512-518. [PMID: 30640118 DOI: 10.1016/j.scitotenv.2018.12.450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 12/09/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
Ammonia (NH3) volatilization is a major loss of nitrogen fertilizer in paddy fields. The incorporation of straw or biochar has been considered to be the alternative options for soil improvement and agriculture sustainability. A field experiment was conducted to evaluate the potential role of rice straw and rice straw derived biochar in controlling NH3 volatilization according to the conventional nitrogen fertilizer level (urea, 270 kg N ha-1) during one rice (Oryza sativa L., cv. Xiushui134) growing season. Four treatments comprised rice straw at the rate of 8 t ha-1 (RS); rice straw derived biochar at the rate of 2.8 t ha-1 (RSBL); rice straw derived biochar at the rate of 22.5 t ha-1 (RSBH) and a control (CK). Compared to straw application, biochar incorporation reduced the cumulative NH3 volatilization (about 20%) from paddy fields significantly (p < 0.05), promoted rice yields and plant N aboveground as well as increased the abundance of ammonia oxidation amoA genes. In contrast with the control, the ratios of NH3-N to total N input for RS, RSBL and RSBH declined significantly 4.15%, 4.40% and 11.12%, respectively (p < 0.05). Reduced NH3 volatilization in RSB treatments were mainly attributed to the decrease of NH4+-N concentration in the surface water, which could resulted from the enhancement of rice growth and the promotion of ammonia oxidation in soil. The increase of soil pH and soil CEC with biochar amendment played important roles in nitrogen retention and nitrogen cycle in soil. These results indicated that the incorporation of rice straw derived biochar instead of rice straw could be a promising approach to controlling NH3 volatilization and improving rice yield.
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Affiliation(s)
- Xue Sun
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Ting Zhong
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Lu Zhang
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Kangshu Zhang
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, 866 Yuhangtang Road, Hangzhou 310058, China.
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50
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Kong Y, Ling N, Xue C, Chen H, Ruan Y, Guo J, Zhu C, Wang M, Shen Q, Guo S. Long-term fertilization regimes change soil nitrification potential by impacting active autotrophic ammonia oxidizers and nitrite oxidizers as assessed by DNA stable isotope probing. Environ Microbiol 2019; 21:1224-1240. [PMID: 30724443 DOI: 10.1111/1462-2920.14553] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 11/19/2018] [Accepted: 01/02/2019] [Indexed: 11/28/2022]
Abstract
Chemoautotrophic ammonia-oxidizers and nitrite-oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long-term fertilization regimes remain largely under-investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers. Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were found to actively respond to urea addition in soils with OF and no fertilizer (CK), whereas only AOB were detected in soils with CF. Around 98% of active AOB were Nitrosospira cluster 3a.1 in all tested soils, and more than 90% of active AOA were Nitrososphaera subcluster 1.1 in unfertilized and organically fertilized soils. Nitrite oxidation was performed only by Nitrospira-like bacteria in all soils. The relative abundances of Nitrospira lineage I and VI were 32% and 61%, respectively, in unfertilized soils, and that of Nitrospira lineage II was 97% in fertilized soils, indicating long-term fertilization shifted the composition of active Nitrospira-like bacteria in response to urea. This finding indicates that different fertilizer regimes impact the composition of active nitrifiers, thus, impacting soil nitrification potential.
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Affiliation(s)
- Yali Kong
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Xue
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huan Chen
- Crop Research Institute, Anhui Academy of Agricultural Science, Hefei, 230031, China
| | - Yang Ruan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junjie Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chen Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
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