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Yang Y, Shen L, Agathokleous E, Wang S, Jin Y, Bai Y, Yang W, Ren B, Jin J, Zhao X. The interplay of soil physicochemical properties, methanogenic diversity, and abundance governs methane production potential in paddy soil subjected to multi-decadal straw incorporation. ENVIRONMENTAL RESEARCH 2024; 256:119246. [PMID: 38810824 DOI: 10.1016/j.envres.2024.119246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/20/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024]
Abstract
Straw incorporation holds significant promise for enhancing soil fertility and mitigating air pollution stemming from straw burning. However, this practice concurrently elevates the production and emission of methane (CH4) from paddy ecosystems. Despite its environmental impact, the precise mechanisms behind the heightened CH4 production resulting from long-term straw incorporation remain elusive. In a 32-year field experiment featuring three fertilization treatments (CFS-chemical fertilizer with wheat straw, CF-chemical fertilizer, and CK-unamended), we investigated the impact of abiotic (soil physicochemical properties) and biotic (methanogenic abundance, diversity, and community composition) factors on CH4 production in paddy fields. Results revealed a significantly higher CH4 production potential under CFS treatment compared to CF and CK treatments. The partial least squares path model revealed that soil physicochemical properties (path coefficient = 0.61), methanogenic diversity (path coefficient = -0.43), and methanogenic abundance (path coefficient = 0.29) collectively determined CH4 production potential, explaining 77% of the variance. Enhanced soil organic carbon content and water content, resulting from straw incorporation, emerged as pivotal factors positively correlated with CH4 production potential. Under CFS treatment, lower Shannon index of methanogens, compared to CF and CK treatments, was attributed to increased Methanosarcina. Notably, the Shannon index and relative abundance of Methanosarcina exhibited negative and positive correlations with CH4 production potential, respectively. Methanogenic abundance, bolstered by straw incorporation, significantly amplified overall potential. This comprehensive analysis underscores the joint influence of abiotic and biotic factors in regulating CH4 production potential during multi-decadal straw incorporation.
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Affiliation(s)
- Yuling Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Lidong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Evgenios Agathokleous
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Shuwei Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yuhan Jin
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yanan Bai
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Wangting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Bingjie Ren
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jinghao Jin
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Xu Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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Bhardwaj L, Kumar D, Singh UP, Joshi CG, Dubey SK. Herbicide application impacted soil microbial community composition and biochemical properties in a flooded rice field. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169911. [PMID: 38185156 DOI: 10.1016/j.scitotenv.2024.169911] [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: 10/08/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
Herbicide application is a common practice in intensive agriculture. However, accumulating herbicide residues in the ecosystem affects important soil attributes. The effect of two herbicides, pendimethalin and pretilachlor, on soil biochemical properties and microbial community composition was studied in a transplanted paddy field. Results reveal a gradual decline in herbicide residue up to 60 days after application. Changes in soil microbiological and biochemical properties (microbial biomass, enzymes, respiration, etc.) showed an inconsistent pattern across the treatments. Quantitative polymerase chain reaction analysis showed the archaeal, bacterial and fungal populations to be of higher order in control soil compared to the treated one. Amplicon sequencing (16S rRNA and ITS genes) exhibited that besides the unclassified genera, ammonia-oxidizing Crenarchaeota and the group represented by Candidatus Nitrososphaera were dominant in both the control and treated samples. Other archaeal genera viz. Methanosarcina and Bathyarchaeia showed a slight decrease in relative abundance of control (0.5 %) compared to the treated soil (0.7 %). Irrespective of treatments, the majority of bacterial genera comprised unclassified and uncultured species, accounting for >64-75 % in the control group and over 78.29 % in the treated samples. Members of Vicinamibacteraceae, Bacillus and Bryobacter were dominant in control samples. Dominant fungal genera belonging to unclassified groups comprised Curvularia, Aspergillus, and Emericellopsis in the control group, whereas Paraphysoderma and Emericellopsis in the herbicide-treated groups. Inconsistent response of soil properties and microbial community composition is evident from the present study, suggesting that the recommended dose of herbicides might not result in any significant change in microbial community composition. The findings of this investigation will help in the formulation of a framework for risk assessment and maintaining sustainable rice cultivation in herbicide- amended soils.
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Affiliation(s)
- Laliteshwari Bhardwaj
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre, Government of Gujarat, Gandhinagar, Gujarat 382011, India
| | - Udai P Singh
- Department of Agronomy, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Government of Gujarat, Gandhinagar, Gujarat 382011, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
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Bhardwaj L, Reddy B, Dubey SK. Deciphering insights into rhizospheric microbial community and soil parameters under the influence of herbicides in zero-tillage tropical rice-agroecosystem. ENVIRONMENTAL RESEARCH 2023; 237:117033. [PMID: 37660873 DOI: 10.1016/j.envres.2023.117033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
Extensive use of chemicals like herbicides in rice and other fields to manage weeds is expected to have a lasting influence on the soil environment. Considering this rationale, we aimed to decipher the effects of herbicides, Pendimethalin and Pretilachlor, applied at 0.5 and 0.6 kg ha-1, respectively on the rhizosphere microbial community and soil characteristics in the tropical rice field, managed under zero tillage cultivation. The quantity of herbicide residues declined gradually since application up to 60 days thereafter it reached the non-detectable level. Most of the soil variables viz., microbial biomass, soil enzymes etc., exhibited slight reduction in the treated soils compared to the control. A gradual decline was observed in Mineral-N, MBC, MBN and enzyme activities. Quantitative polymerase chain reaction results showed maximal microbial abundance of bacteria, fungi and archaea at mid-flowering stage of rice crop. The 16 rRNA and ITS region targeted amplicons high throughput sequencing microbial metagenomic approach revealed total of 94, 1353, and 510 species for archaea, bacteria and fungi, respectively. The metabarcoding of core microbiota revealed that the archaea comprised of Nitrososphaera, Nitrosocosmicus, and Methanosarcina. In the bacterial core microbiome, Neobacillus, Nitrospira, Thaurea, and Microvigra were found as the predominant taxa. Fusarium, Clonostachys, Nigrospora, Mortierella, Chaetomium, etc., were found in core fungal microbiome. Overall, the study exhibited that the recommended dose of herbicides found to be detrimental to the microbial dynamics, though a negative relation between residues and soil variables was observed that might alter the microbial diversity. The outcomes offer a comprehensive understanding of how herbicides affect the microbial community in zero tillage rice soil, thus has a critical imputation for eco-friendly and sustainable rice agriculture. Further, the long-term studies will be helpful in elucidating the role of identified microbial groups in sustaining the soil fertility and crop productivity.
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Affiliation(s)
- Laliteshwari Bhardwaj
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Bhaskar Reddy
- Virus Research and Diagnostic Laboratory, Government Institute of Medical Sciences, Greater Noida, Uttar Pradesh-9, 201310, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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Xu C, Shen S, Zhou B, Feng Y, He Z, Shi L, Wang Y, Wang H, Mishra T, Xue L. Long-term non-phosphorus application increased paddy methane emission by promoting organic acid and methanogen abundance in Tai Lake region, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161146. [PMID: 36566847 DOI: 10.1016/j.scitotenv.2022.161146] [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: 06/20/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Rice paddy is a significant source of atmospheric methane (CH4), a major global warming source. CH4 emission from paddy fields is greatly influenced by phosphorus (P) management, especially the long-term non-P application on CH4 emission is largely unexplored. In the present study, long-term non-P application (NK) and P application (NPK) treatments of two paddy fields in Suzhou (from 1980) and Yixing (from 2009), Tai Lake region was done. The effect of P application on CH4 emissions and related microorganisms (i.e., methanogens and methanotrophs) from 2019 to 2020 was analyzed. Results revealed that long-term NK treatment didn't alter the seasonal trend of CH4 flux, but significantly promoted CH4 emissions at the tillering stage. The non-P application for >12 years caused the cumulative CH4 emissions of NK treatment in the whole rice season significantly increased by 41.9-221 % in two fields compared to NPK treatment in 2019 and 2020. NK treatment increased the abundance and diversity of methanogens, while reducing the abundance and diversity of methanotrophs. Community composition of soil pmoA gene differed in two experiment sites. Correlation analysis revealed that the CH4 emission was significant and positively related to soil mcrA gene and C/P while negatively related to soil pmoA gene and P. Structure equation model analysis show the low soil available P content was the dominant driving factor for the high CH4 emission under long-term non-P application through its direct impact on soil mcrA and pmoA genes. The increased soil organic acid content was another driver which was positively related to soil mcrA gene and negatively to soil pmoA gene. Our findings demonstrate the important role of soil P in regulating CH4 emissions from paddy fields in the Tai Lake region, China, and suitable P application is necessary for ensuring the yield while reducing CH4 emission.
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Affiliation(s)
- Chen Xu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212001, China
| | - Susu Shen
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Beibei Zhou
- College of Environment and Ecology, Jiangsu Open University, Nanjing 210017, China
| | - Yuanyuan Feng
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhu He
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Linlin Shi
- National Agricultural Experimental Station for Soil Quality, Suzhou Academy of Agricultural Sciences, Suzhou 215105, China
| | - Yu Wang
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Haihou Wang
- National Agricultural Experimental Station for Soil Quality, Suzhou Academy of Agricultural Sciences, Suzhou 215105, China
| | - Tripti Mishra
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lihong Xue
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212001, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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5
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Wang S, Sun P, Zhang G, Gray N, Dolfing J, Esquivel-Elizondo S, Peñuelas J, Wu Y. Contribution of periphytic biofilm of paddy soils to carbon dioxide fixation and methane emissions. Innovation (N Y) 2022; 3:100192. [PMID: 34950915 PMCID: PMC8672048 DOI: 10.1016/j.xinn.2021.100192] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/23/2021] [Indexed: 10/26/2022] Open
Abstract
Rice paddies are major contributors to anthropogenic greenhouse gas emissions via methane (CH4) flux. The accurate quantification of CH4 emissions from rice paddies remains problematic, in part due to uncertainties and omissions in the contribution of microbial aggregates on the soil surface to carbon fluxes. Herein, we comprehensively evaluated the contribution of one form of microbial aggregates, periphytic biofilm (PB), to carbon dioxide (CO2) and CH4 emissions from paddies distributed across three climatic zones, and quantified the pathways that drive net CH4 production as well as CO2 fixation. We found that PB accounted for 7.1%-38.5% of CH4 emissions and 7.2%-12.7% of CO2 fixation in the rice paddies. During their growth phase, PB fixed CO2 and increased the redox potential, which promoted aerobic CH4 oxidation. During the decay phase, PB degradation reduced redox potential and increased soil organic carbon availability, which promoted methanogenic microbial community growth and metabolism and increased CH4 emissions. Overall, PB acted as a biotic converter of atmospheric CO2 to CH4, and aggravated carbon emissions by up to 2,318 kg CO2 equiv ha-1 season-1. Our results provide proof-of-concept evidence for the discrimination of the contributions of surface microbial aggregates (i.e., PB) from soil microbes, and a profound foundation for the estimation and simulation of carbon fluxes in a potential novel approach to the mitigation of CH4 emissions by manipulating PB growth.
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Affiliation(s)
- Sichu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Shuitianba Zigui, Yichang 443605, China.,College of Advanced Agricultural Science, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Pengfei Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Guangbin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Neil Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle upon Tyne NE1 8QH, UK
| | - Sofia Esquivel-Elizondo
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Josep Peñuelas
- Consejo Superior de Investigaciones Científicas (CSIC), Global Ecology Unit, Centre for Ecological Research and Forestry Applications (CREAF)-CSIC-Universitat Autonoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Catalonia, Spain
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Shuitianba Zigui, Yichang 443605, China
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Wang Y, Hu Z, Shen L, Liu C, Islam ARMT, Wu Z, Dang H, Chen S. The process of methanogenesis in paddy fields under different elevated CO 2 concentrations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145629. [PMID: 33940739 DOI: 10.1016/j.scitotenv.2021.145629] [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: 12/08/2020] [Revised: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Understanding the process of methanogenesis in paddy fields under the scenarios of future climate change is of great significance for reducing greenhouse gas emissions and regulating the soil carbon cycle. Methyl Coenzyme M Reductase subunit A (mcrA) of methanogens is a rate-limiting enzyme that catalyzes the final step of CH4 production. However, the mechanism of methanogenesis change in the paddy fields under different elevated CO2 concentrations (e[CO2]) is rarely explored in earlier studies. In this research, we explored how the methanogens affect CH4 flux in paddy fields under various (e[CO2]). CH4 flux and CH4 production potential (MPP), and mcrA gene abundance were quantitatively analyzed under C (ambient CO2 concentration), C1 (C + 160 ppm CO2), and C2 (C + 200 ppm CO2) treatments. Additionally, the community composition and structure of methanogens were also compared with Illumina MiSeq sequencing. The results showed that C2 treatment significantly increased CH4 flux and MPP at the tillering stage. E[CO2] had a positive effect on the abundance of methanogens, but the effect was insignificant. We detected four known dominant orders of methanogenesis in this study, such as Methanosarcinales, Methanobacteriales, Methanocellales, and Methanomicrobiales. Although e[CO2] did not significantly change the overall community structure and diversity of methanogens, C2 treatment significantly reduced the relative abundance of two uncultured genera compared to C treatment. A linear regression model of DOC, methanogenic abundance, and MPP can explain 67.2% of the variation of CH4 flux under e[CO2]. Overall, our results demonstrated that CH4 flux in paddy fields under e[CO2] was mainly controlled by soil unstable C substrate and the abundance and activity of methanogens in rhizosphere soil.
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Affiliation(s)
- Yuanyuan Wang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Zhenghua Hu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China.
| | - Lidong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China.
| | - Chao Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - A R M Towfiqul Islam
- Department of Disaster Management, Disaster Management E-Learning Centre, Begum Rokeya University, Rangpur 5400, Bangladesh
| | - Zhurong Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Huihui Dang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Shutao Chen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
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Gupta K, Kumar R, Baruah KK, Hazarika S, Karmakar S, Bordoloi N. Greenhouse gas emission from rice fields: a review from Indian context. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:30551-30572. [PMID: 33905059 DOI: 10.1007/s11356-021-13935-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Agricultural soil acts as a source and sink of important greenhouse gases (GHGs) like methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2). Rice paddies have been a major concern to scientific community, because they produce the threatening and long-lasting GHGs mainly CH4 and N2O. Around 30% and 11% of global agricultural CH4 and N2O, respectively, emitted from rice fields. Thus, it is urgent to concurrently quantify the fluxes of CH4 and N2O to improve understanding of both the gases from rice fields and to develop mitigation strategies for upcoming climate change reduction. An effort is being made in this review to discuss exclusively the emission of CH4 and N2O under normal and controlled conditions in different locations of India and also addresses the current synthesis of available data on how field and crop management activities influence CH4 and N2O emissions in rice fields. Making changes to conventional crop management regimes could have a significant impact on reducing GHG emissions from rice field. Environmental and agricultural factors related to soil could be easily altered by management practices. So, knowing the mechanism of CH4 and N2O production and release in the rice field and factors controlling the emissions is fundamental to develop well-organized strategies to reduce emissions from rice cultivated soil. This will help the regulatory bodies or policy makers to formulate adequate policies for agricultural farmers to refine the GHG emissions as well as minimize the global climate change.
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Affiliation(s)
- Khushboo Gupta
- Department of Environmental Sciences, Central University of Jharkhand, Brambe, Ranchi, 835205, India
| | - Raushan Kumar
- Department of Environmental Sciences, Central University of Jharkhand, Brambe, Ranchi, 835205, India
| | - Kushal Kumar Baruah
- School of Earth and Environmental Sciences, Royal Global University, Guwahati, Assam, 781035, India
| | - Samarendra Hazarika
- ICAR Research Complex for NEH Region, Umiam, Guwahati, Meghalaya, 793103, India
| | - Susmita Karmakar
- Department of Environmental Sciences, Central University of Jharkhand, Brambe, Ranchi, 835205, India
| | - Nirmali Bordoloi
- Department of Environmental Sciences, Central University of Jharkhand, Brambe, Ranchi, 835205, India.
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8
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Jung J, Kim JS, Taffner J, Berg G, Ryu CM. Archaea, tiny helpers of land plants. Comput Struct Biotechnol J 2020; 18:2494-2500. [PMID: 33005311 PMCID: PMC7516179 DOI: 10.1016/j.csbj.2020.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/01/2020] [Accepted: 09/05/2020] [Indexed: 01/02/2023] Open
Abstract
Archaea are members of most microbiomes. While archaea are highly abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome. Only a few studies have investigated the role of archaea in plant health and its potential symbiosis in ecosystems. This review discusses recent progress in identifying how archaea contribute to plant traits such as growth, adaptation to abiotic stresses, and immune activation. We synthesized the most recent functional and molecular data on archaea, including root colonization and the volatile emission to activate plant systemic immunity. These data represent a paradigm shift in our understanding of plant-microbiota interactions.
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Affiliation(s)
- Jihye Jung
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, South Korea
- Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | - Jun-Seob Kim
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, South Korea
| | - Julian Taffner
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, South Korea
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9
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Imchen M, Kumavath R, Vaz ABM, Góes-Neto A, Barh D, Ghosh P, Kozyrovska N, Podolich O, Azevedo V. 16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages. Front Microbiol 2019; 10:2103. [PMID: 31616390 PMCID: PMC6764247 DOI: 10.3389/fmicb.2019.02103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/26/2019] [Indexed: 11/21/2022] Open
Abstract
Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Ranjith Kumavath
- Department of Genomic Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Aline B M Vaz
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India
| | - Preetam Ghosh
- Department of Computer Sciences, Virginia Commonwealth University, Richmond, VA, United States
| | - Natalia Kozyrovska
- Institute of Molecular Biology and Genetics, National Academy of Sciences, Kyiv, Ukraine
| | - Olga Podolich
- Institute of Molecular Biology and Genetics, National Academy of Sciences, Kyiv, Ukraine
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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10
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Vishwakarma P, Dubey SK. Diversity of endophytic bacterial community inhabiting in tropical aerobic rice under aerobic and flooded condition. Arch Microbiol 2019; 202:17-29. [DOI: 10.1007/s00203-019-01715-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 08/03/2019] [Accepted: 08/13/2019] [Indexed: 11/29/2022]
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11
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Yuan J, Yuan Y, Zhu Y, Cao L. Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:770-781. [PMID: 29426201 DOI: 10.1016/j.scitotenv.2018.01.233] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Paddy soil accounts for 10% of global atmospheric methane (CH4) emissions. Many types of fertilizers may enhance CH4 emissions, especially organic fertilizer. The aim of this study was to explore the effects of different fertilizers on CH4 and methanogen patterns in paddy soil. This experiment involved four treatments: chemical fertilizer (CT), organic fertilizer (OT), mixed with chemical and organic fertilizer (MT), and no fertilizer (ctrl). The three fertilization treatments were applied with total nitrogen at the same rate of 300 kg N ha-1. Paddy CH4, soil physicochemical variables and methanogen communities were quantitatively analyzed. Rhizosphere soil mcrA and pmoA gene copy numbers were determined by qPCR. Methanogenic 16S rRNA genes were identified by MiSeq sequencing. The results indicated CH4 emissions were significantly higher in OT (145.31 kg ha-1) than MT (84.62 kg ha-1), CT (77.88 kg ha-1) or ctrl (32.19 kg ha-1). Soil organic acids were also increased by organic fertilization. CH4 effluxes were significantly and negatively related to mcrA and pmoA gene copy numbers, and positively related to mcrA/pmoA. Above all, hydrogenotrophic Methanocella and acetoclastic Methanosaeta were the predominant methanogenic communities; these communities were strictly associated with soil potassium, oxalate, acetate, and succinate. Application of organic fertilizer promoted the dominant acetoclastic methanogens, but suppressed the dominant hydrogenotrophic methanogens. The transformation in methanogenic community structure and enhanced availability of C substrates may explain the increased CH4 production in OT compared to other treatments. Compared to OT, MT may partially mitigate CH4 emissions while guaranteeing a high rice yield. On this basis, we recommend the local fertilization pattern should change from 300 N kg ha-1 of organic manure to the same level of mixed fertilization. Moreover, we suggest multiple combinations of mixed fertilization merit more investigation in the future.
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Affiliation(s)
- Jing Yuan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yongkun Yuan
- Irrigation Technology Extension Station of Qingpu, 2 Yuan Road, Shanghai 201707, China
| | - Yihang Zhu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Linkui Cao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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12
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Jeong ST, Kim GW, Hwang HY, Kim PJ, Kim SY. Beneficial effect of compost utilization on reducing greenhouse gas emissions in a rice cultivation system through the overall management chain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:115-122. [PMID: 28910713 DOI: 10.1016/j.scitotenv.2017.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/01/2017] [Accepted: 09/01/2017] [Indexed: 05/15/2023]
Abstract
Livestock manure application can stimulate greenhouse gas (GHG) emissions, especially methane (CH4) in rice paddy. The stabilized organic matter (OM) is recommended to suppress CH4 emission without counting the additional GHG emission during the composting process. To evaluate the effect of compost utilization on the net global warming potential (GWP) of a rice cropping system, the fluxes of GHGs from composting to land application were calculated by a life cycle assessment (LCA) method. The model framework was composed of GHG fluxes from industrial activities and biogenic GHG fluxes from the composting and rice cultivation processes. Fresh manure emitted 30MgCO2-eq.ha-1, 90% and 10% of which were contributed by CH4 and nitrous oxide (N2O) fluxes, respectively, during rice cultivation. Compost utilization decreased net GWP by 25% over that of the fresh manure during the whole process. The composting process increased the GWP of the industrial processes by 35%, but the 60% reduction in CH4 emissions from the rice paddy mainly influenced the reduction of GWP during the overall process. Therefore, compost application could be a good management strategy to reduce GHG emissions from rice paddy systems.
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Affiliation(s)
- Seung Tak Jeong
- Division of Applied Life Science (BK 21+ Program), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gil Won Kim
- Division of Applied Life Science (BK 21+ Program), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hyun Young Hwang
- Division of Applied Life Science (BK 21+ Program), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Pil Joo Kim
- Division of Applied Life Science (BK 21+ Program), Gyeongsang National University, Jinju 52828, Republic of Korea; Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Sang Yoon Kim
- National Academy of Agricultural Science, Rural Development Administration, Wanju 55365, Republic of Korea.
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13
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Vaksmaa A, van Alen TA, Ettwig KF, Lupotto E, Valè G, Jetten MSM, Lüke C. Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil. Front Microbiol 2017; 8:2127. [PMID: 29180985 PMCID: PMC5693880 DOI: 10.3389/fmicb.2017.02127] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/18/2017] [Indexed: 11/30/2022] Open
Abstract
Paddy fields are important ecosystems, as rice is the primary food source for about half of the world's population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60 cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic 13C-CH4 turnover with a suite of electron acceptors. The bacterial community consisted mainly of Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes, and Actinobacteria. Among archaea, Euryarchaeota and Bathyarchaeota dominated over Thaumarchaeota in the upper 30 cm of the soil. Bathyarchaeota constituted up to 45% of the total archaeal reads in the top 5 cm. In the methanogenic community, Methanosaeta were generally more abundant than the versatile Methanosarcina. The measured maximum methane production rate was 444 nmol gdwh-1, and the maximum rates of nitrate-, nitrite-, and iron-dependent anaerobic oxidation of methane (AOM) were 57 nmol, 55 nmol, and 56 nmol gdwh-1, respectively, at different depths. qPCR revealed a higher abundance of 'Candidatus Methanoperedens nitroreducens' than methanotrophic NC10 phylum bacteria at all depths, except at 60 cm. These results demonstrate that there is substantial potential for AOM in fertilized paddy fields, with 'Candidatus Methanoperedens nitroreducens' archaea as a potential important contributor.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Theo A. van Alen
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Katharina F. Ettwig
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Elisabetta Lupotto
- Research Centre for Food and Nutrition, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Rome, Italy
| | - Giampiero Valè
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Mike S. M. Jetten
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Claudia Lüke
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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14
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Alpana S, Vishwakarma P, Adhya TK, Inubushi K, Dubey SK. Molecular ecological perspective of methanogenic archaeal community in rice agroecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 596-597:136-146. [PMID: 28431358 DOI: 10.1016/j.scitotenv.2017.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/02/2017] [Accepted: 04/02/2017] [Indexed: 06/07/2023]
Abstract
Methane leads to global warming owing to its warming potential higher than carbon dioxide (CO2). Rice fields represent the major source of methane (CH4) emission as the recent estimates range from 34 to 112 Tg CH4 per year. Biogenic methane is produced by anaerobic methanogenic archaea. Advances in high-throughput sequencing technologies and isolation methodologies enabled investigators to decipher methanogens to be unexpectedly diverse in phylogeny and ecology. Exploring the link between biogeochemical methane cycling and methanogen community dynamics can, therefore, provide a more effective mechanistic understanding of CH4 emission from rice fields. In this review, we summarize the current knowledge on the diversity and activity of methanogens, factors controlling their ecology, possible interactions between rice plants and methanogens, and their potential involvement in the source relationship of greenhouse gas emissions from rice fields.
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Affiliation(s)
- Singh Alpana
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - P Vishwakarma
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - T K Adhya
- School of Biotechnology, KIIT University, Bhubaneshwar 751024, India
| | - K Inubushi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 2718510, Japan
| | - S K Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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15
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Liu Y, Liu X, Cheng K, Li L, Zhang X, Zheng J, Zheng J, Pan G. Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO 2 and Temperature in a Paddy Field. Front Microbiol 2016; 7:1895. [PMID: 27933055 PMCID: PMC5121223 DOI: 10.3389/fmicb.2016.01895] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/11/2016] [Indexed: 11/13/2022] Open
Abstract
Although climate change is predicted to affect methane (CH4) emissions in paddy soil, the dynamics of methanogens and methanotrophs in paddy fields under climate change have not yet been fully investigated. To address this issue, a multifactor climate change experiment was conducted in a Chinese paddy field using the following experimental treatments: (1) enrichment of atmospheric CO2 concentrations (500 ppm, CE), (2) canopy air warming (2°C above the ambient, WA), (3) combined CO2 enrichment and warming (CW), and (4) ambient conditions (CK). We analyzed the abundance of methanogens and methanotrophs, community structures, CH4 production and oxidation potentials, in situ CH4 emissions using real-time PCR, T-RFLP, and clone library techniques, as well as biochemical assays. Compared to the control under CE and CW treatments, CH4 production potential, methanogenic gene abundance and soil microbial biomass carbon significantly increased; the methanogenic community, however, remained stable. The canopy air warming treatment only had an effect on CH4 oxidation potential at the ripening stage. Phylogenic analysis indicated that methanogens in the rhizosphere were dominated by Methanosarcina, Methanocellales, Methanobacteriales, and Methanomicrobiales, while methanotrophic sequences were classified as Methylococcus, Methylocaldum, Methylomonas, Methylosarcina (Type I) and Methylocystis (Type II). However, the relative abundance of Methylococcus (Type I) decreased under CE and CW treatments and the relative abundance of Methylocystis (Type II) increased. The in situ CH4 fluxes indicated similar seasonal patterns between treatments; both CE and CW increased CH4 emissions. In conclusion results suggest that methanogens and methanotrophs respond differently to elevated atmospheric CO2 concentrations and warming, thus adding insights into the effects of simulated global climate change on CH4 emissions in paddy fields.
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Affiliation(s)
- Yuan Liu
- Department of Bioengineering, College of Life Science, Huaibei Normal University Huaibei, China
| | - Xiaoyu Liu
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Kun Cheng
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Lianqing Li
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Xuhui Zhang
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Jufeng Zheng
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Jinwei Zheng
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Genxing Pan
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural UniversityNanjing, China; Zhejiang Provincial Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration, School of Environmental and Resource Sciences, Zhejiang A & F University, Lin'anHangzhou, China
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16
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Espenberg M, Truu M, Truu J, Maddison M, Nõlvak H, Järveoja J, Mander Ü. Impact of Reed Canary Grass Cultivation and Mineral Fertilisation on the Microbial Abundance and Genetic Potential for Methane Production in Residual Peat of an Abandoned Peat Extraction Area. PLoS One 2016; 11:e0163864. [PMID: 27684377 PMCID: PMC5042519 DOI: 10.1371/journal.pone.0163864] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/15/2016] [Indexed: 12/19/2022] Open
Abstract
This study examined physiochemical conditions and prokaryotic community structure (the bacterial and archaeal 16S rRNA genes and mcrA gene abundances and proportions), and evaluated the effect of reed canary grass cultivation and mineral fertilisation on these factors, in the 60 cm thick residual peat layer of experimental plots located on an abandoned peat extraction area. The archaeal proportion was 0.67-39.56% in the prokaryotic community and the methanogens proportion was 0.01-1.77% in the archaeal community. When bacterial abundance was higher in the top 20 cm of peat, the archaea were more abundant in the 20-60 cm layer and methanogens in the 40-60 cm layer of the residual peat. The bacterial abundance was significantly increased, but archaeal abundance was not affected by cultivation. The fertiliser application had a slight effect on peat properties and on archaeal and methanogen abundances in the deeper layer of cultivated peat. The CH4 emission was positively related to mcrA abundance in the 20-60 cm of the bare peat, while in case of reed canary grass cultivation these two parameters were not correlated. Reed canary grass cultivation mitigated CH4 emission, although methanogen abundance remained approximately the same or even increased in different layers of residual peat under cultivated sites over time. This study supports the outlook of using abandoned peat extraction areas to produce reed canary grass for energy purposes as an advisable land-use practice from the perspective of atmospheric impact in peatland-rich Northern Europe.
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Affiliation(s)
- Mikk Espenberg
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Marika Truu
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jaak Truu
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Maddison
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Hiie Nõlvak
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Järvi Järveoja
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ülo Mander
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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17
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Primers: Functional Genes and 16S rRNA Genes for Methanogens. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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18
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Kim SY, Pramanik P, Bodelier PLE, Kim PJ. Cattle Manure Enhances Methanogens Diversity and Methane Emissions Compared to Swine Manure under Rice Paddy. PLoS One 2014; 9:e113593. [PMID: 25494364 PMCID: PMC4262209 DOI: 10.1371/journal.pone.0113593] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/29/2014] [Indexed: 11/19/2022] Open
Abstract
Livestock manures are broadly used in agriculture to improve soil quality. However, manure application can increase the availability of organic carbon, thereby facilitating methane (CH4) production. Cattle and swine manures are expected to have different CH4 emission characteristics in rice paddy soil due to the inherent differences in composition as a result of contrasting diets and digestive physiology between the two livestock types. To compare the effect of ruminant and non-ruminant animal manure applications on CH4 emissions and methanogenic archaeal diversity during rice cultivation (June to September, 2009), fresh cattle and swine manures were applied into experimental pots at 0, 20 and 40 Mg fresh weight (FW) ha-1 in a greenhouse. Applications of manures significantly enhanced total CH4 emissions as compared to chemical fertilization, with cattle manure leading to higher emissions than swine manure. Total organic C contents in cattle (466 g kg-1) and swine (460 g kg-1) manures were of comparable results. Soil organic C (SOC) contents were also similar between the two manure treatments, but dissolved organic C (DOC) was significantly higher in cattle than swine manure. The mcrA gene copy numbers were significantly higher in cattle than swine manure. Diverse groups of methanogens which belong to Methanomicrobiaceae were detected only in cattle-manured but not in swine-manured soil. Methanogens were transferred from cattle manure to rice paddy soils through fresh excrement. In conclusion, cattle manure application can significantly increase CH4 emissions in rice paddy soil during cultivation, and its pretreatment to suppress methanogenic activity without decreasing rice productivity should be considered.
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Affiliation(s)
- Sang Yoon Kim
- Division of Applied Life Science (BK 21 Program), Gyeongsang National University, Jinju, South Korea
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, The Netherlands
| | - Prabhat Pramanik
- Division of Applied Life Science (BK 21 Program), Gyeongsang National University, Jinju, South Korea
| | - Paul L. E. Bodelier
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, The Netherlands
| | - Pil Joo Kim
- Division of Applied Life Science (BK 21 Program), Gyeongsang National University, Jinju, South Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
- * E-mail:
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19
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Lee HJ, Kim SY, Kim PJ, Madsen EL, Jeon CO. Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem. FEMS Microbiol Ecol 2014; 88:195-212. [DOI: 10.1111/1574-6941.12282] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 01/03/2014] [Accepted: 01/03/2014] [Indexed: 01/19/2023] Open
Affiliation(s)
- Hyo Jung Lee
- Department of Life Science; Chung-Ang University; Seoul Korea
| | - Sang Yoon Kim
- Division of Applied Life Science; Gyeongsang National University; Jinju Korea
| | - Pil Joo Kim
- Division of Applied Life Science; Gyeongsang National University; Jinju Korea
| | | | - Che Ok Jeon
- Department of Life Science; Chung-Ang University; Seoul Korea
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20
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Ke X, Lu Y, Conrad R. Different behaviour of methanogenic archaea and Thaumarchaeota in rice field microcosms. FEMS Microbiol Ecol 2013; 87:18-29. [PMID: 23909555 DOI: 10.1111/1574-6941.12188] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/26/2013] [Accepted: 07/26/2013] [Indexed: 11/27/2022] Open
Abstract
Archaea in rice fields play an important role in carbon and nitrogen cycling. They comprise methane-producing Euryarchaeota as well as ammonia-oxidizing Thaumarchaeota, but their community structures and population dynamics have not yet been studied in the same system. Different soil compartments (surface, bulk, rhizospheric soil) and ages of roots (young and old roots) at two N fertilization levels and at three time points (the panicle initiation, heading and maturity periods) of the season were assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of archaeal genes (mcrA, amoA, 16S rRNA gene). The community of total Archaea in soil and root samples mainly consisted of the methanogens and the Thaumarchaeota and their abundance increased over the season. Methanogens proliferated everywhere, but Thaumarchaeota proliferated only on the roots and in response to nitrogen fertilization. The community structures of Archaea, methanogens and Thaumarchaeota were different in soil and root samples indicating niche differentiation. While Methanobacteriales were generally present, Methanosarcinaceae and Methanocellales were the dominant methanogens in soil and root samples, respectively. The results emphasize the specific colonization of roots by two ecophysiologically different groups of archaea which may belong to the core root biome.
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Affiliation(s)
- Xiubin Ke
- College of Resources and Environment Sciences, China Agricultural University, Beijing, China; Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Biotechnology, Ministry of Agriculture, Beijing, China
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