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Gontijo JB, Paula FS, Bieluczyk W, França AG, Navroski D, Mandro JA, Venturini AM, Asselta FO, Mendes LW, Moura JMS, Moreira MZ, Nüsslein K, Bohannan BJM, Bodelier PLE, Rodrigues JLM, Tsai SM. Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios. ENVIRONMENTAL MICROBIOME 2024; 19:48. [PMID: 39020395 PMCID: PMC11256501 DOI: 10.1186/s40793-024-00596-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024]
Abstract
Seasonal floodplains in the Amazon basin are important sources of methane (CH4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH4 fluxes. CH4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH4 oxidation pathways in mitigating CH4 emissions in Amazonian floodplains.
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Affiliation(s)
- Júlia B Gontijo
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil.
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA.
| | - Fabiana S Paula
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Wanderlei Bieluczyk
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Aline G França
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Deisi Navroski
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Jéssica A Mandro
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | | | - Fernanda O Asselta
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Lucas W Mendes
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - José M S Moura
- Instituto de Formação Interdisciplinar e Intercultural, Universidade Federal do Oeste do Pará, Santarém, PA, Brazil
| | - Marcelo Z Moreira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Paul L E Bodelier
- Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, GE, The Netherlands
| | - Jorge L Mazza Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Siu M Tsai
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
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2
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Shulman HB, Aronson EL, Dierick D, Pinto‐Tomás AA, Botthoff JK, Artavia‐León A, Allen MF. Leafcutter ants enhance microbial drought resilience in tropical forest soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13251. [PMID: 38778789 PMCID: PMC11112399 DOI: 10.1111/1758-2229.13251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/15/2024] [Indexed: 05/25/2024]
Abstract
We conducted a research campaign in a neotropical rainforest in Costa Rica throughout the drought phase of an El-Nino Southern Oscillation event to determine microbial community dynamics and soil C fluxes. Our study included nests of the leafcutter ant Atta cephalotes, as soil disturbances made by these ecosystem engineers may influence microbial drought response. Drought decreased the diversity of microbes and the abundance of core microbiome taxa, including Verrucomicrobial bacteria and Sordariomycete fungi. Despite initial responses of decreasing diversity and altered composition, 6 months post-drought the microbiomes were similar to pre-drought conditions, demonstrating the resilience of soil microbial communities to drought events. A. cephalotes nests altered fungal composition in the surrounding soil, and reduced both fungal mortality and growth of Acidobacteria post-drought. Drought increased CH4 consumption in soils due to lower soil moisture, and A. cephalotes nests decrease the variability of CH4 emissions in some soil types. CH4 emissions were tracked by the abundance of methanotrophic bacteria and fungal composition. These results characterize the microbiome of tropical soils across both time and space during drought and provide evidence for the importance of leafcutter ant nests in shaping soil microbiomes and enhancing microbial resilience during climatic perturbations.
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Affiliation(s)
- Hannah B. Shulman
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Emma L. Aronson
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
- Center for Conservation BiologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Diego Dierick
- Department of Biological SciencesFlorida International UniversityMiamiFloridaUSA
| | - Andrian A. Pinto‐Tomás
- Centro De Investigación En Estructuras MicroscópicasUniversidad de Costa RicaSan JoséCosta Rica
| | - Jon K. Botthoff
- Center for Conservation BiologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Allan Artavia‐León
- Centro De Investigación En Estructuras MicroscópicasUniversidad de Costa RicaSan JoséCosta Rica
| | - Michael F. Allen
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
- Center for Conservation BiologyUniversity of CaliforniaRiversideCaliforniaUSA
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3
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Diversity of gut methanogens and functional enzymes associated with methane metabolism in smallholder dairy cattle. Arch Microbiol 2022; 204:608. [PMID: 36075991 DOI: 10.1007/s00203-022-03187-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/02/2022]
Abstract
Methane is a greenhouse gas with disastrous consequences when released to intolerable levels. Ruminants produce methane during gut fermentation releasing it through belching and/or flatulence. To better understand the diversity of methanogens and functional enzymes associated with methane metabolism in dairy cows, 48 samples; 6 rumen fluid and 42 dung samples were collected from Kenyan and Tanzanian farms and were analyzed using shotgun metagenomic approach. Statistical analysis for species frequency, relative abundance, percentages, and P values were undertaken using MS Excel and IBM SPSS statistics 20. The results showed archaea from 5 phyla, 9 classes, 16 orders, 25 families, 59 genera, and 87 species. Gut sites significantly contributed to the presence and distribution of various methanogens (P < 0.01). The class Methanomicrobia was abundant in the rumen samples (~ 39%) and dung (~ 44%). The most abundant (~ 17%) methanogen species identified was Methanocorpusculum labreanum. However, some taxonomic class data were unclassified (~ 6% in the rumen and ~ 4% in the dung). Five functional enzymes: Glycine/Serine hydroxymethyltransferase, Formylmethanofuran-tetrahydromethanopterin N-formyltransferase, Formate dehydrogenase, anaerobic carbon monoxide dehydrogenase, and catalase-peroxidase associated with methane metabolism were identified. KEGG functional metabolic analysis for the enzymes identified during this study was significant (P < 0.05) for five metabolism processes. The methanogen species abundances from this study in numbers/kind can be utilized exclusively or jointly as indirect selection criteria for methane mitigation. When targeting functional genes of the microbes/animal for better performance, the concern not to affect the host animal's functionality should be undertaken. Future studies should consider taxonomically categorizing unclassified species.
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4
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Pausan MR, Blohs M, Mahnert A, Moissl-Eichinger C. The sanitary indoor environment-a potential source for intact human-associated anaerobes. NPJ Biofilms Microbiomes 2022; 8:44. [PMID: 35650275 PMCID: PMC9160270 DOI: 10.1038/s41522-022-00305-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/04/2022] [Indexed: 02/06/2023] Open
Abstract
A healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. People in high-income countries spend most of their time indoors and for this reason, the built environment (BE) might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes. We sampled the bathrooms in ten households and used propidium monoazide (PMA) to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses. Quantitative and qualitative analysis revealed that most of the microbial taxa in the BE samples are human-associated. Less than 25% of the prokaryotic signatures originate from intact cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. However, we also confirmed the presence of intact, strictly anaerobic taxa on bathroom floors, including methanogenic archaea. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that human-associated methanogens can survive oxic conditions for at least 6 h. We collected strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.
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Affiliation(s)
- Manuela-Raluca Pausan
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Steigerwald Arzneimittelwerk GmbH, Bayer Consumer Health, Darmstadt, Germany
| | - Marcus Blohs
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
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Han Q, Guo H, Zhang J, Huang Z, Urynowicz MA, Ali MI. Methane Generation from Anthracite by Fungi and Methanogen Mixed Flora Enriched from Produced Water Associated with the Qinshui Basin in China. ACS OMEGA 2021; 6:31935-31944. [PMID: 34870016 PMCID: PMC8638023 DOI: 10.1021/acsomega.1c04705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Biogenic coalbed methane (CBM) is generally believed to be formed by anaerobic bacteria and methanogens, while a few studies took fungi into account. Here, the microflora consisting of fungi and methanogens was enriched from the produced water associated with the Qinshui Basin using anthracite as the only carbon source. The maximum methane yield of 231 μmol/g coal was obtained after 22 days of cultivation under the optimum temperature of 35 °C, pH of 8, salinity of 0-2%, particle size of 0.075-0.150 mm, and the solid-liquid ratio of 1:30. It could remain active even after exposure to air for 24 h. Miseq results showed that the archaea were mainly composed of Methanocella, a hydrogenotrophic methanogen, followed by acetoclastic methanogen Methanosaeta and Methanosarcina, which could use various methanogenic substrates. The fungal communities mainly included Amorphotheca, Alternaria, Aspergillus, and Penicilium, which are all able to degrade complex organics such as aromatics and lignin. After cultivation, the crystal structure of anthracite became looser, as shown by XRD results, which might be due to the swelling effect caused by the destruction of the aromatic ring structure of coal under the function of fungi. The stretching vibration intensity of each functional group in coal decreased with cultivation, as revealed by FTIR. The GC-MS results showed that the concentration of alkanes and alcohols decreased significantly, which are the products of ring-opening of aromatics by fungi. These results suggested that fungi and methanogens in the coalbed also can syntrophically degrade coal effectively, especially for aromatics in coal.
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Affiliation(s)
- Qing Han
- College
of Safety and Emergency Management and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
| | - Hongguang Guo
- College
of Safety and Emergency Management and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
- Key
Lab of In-Situ Property-Improving Mining of Ministry of Education, Taiyuan University of Technology, Taiyuan 030024, China
| | - Jinlong Zhang
- College
of Safety and Emergency Management and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
| | - Zaixing Huang
- School
of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou 221116, China
- Department
of Civil & Architectural Engineering, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Michael Allan Urynowicz
- Department
of Civil & Architectural Engineering, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Muhammad Ishtiaq Ali
- Environmental
Microbiology Lab, Department of Microbiology, Quaid-I-Azam University, Islamabad 45320, Pakistan
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Lyautey E, Billard E, Tissot N, Jacquet S, Domaizon I. Seasonal Dynamics of Abundance, Structure, and Diversity of Methanogens and Methanotrophs in Lake Sediments. MICROBIAL ECOLOGY 2021; 82:559-571. [PMID: 33538855 DOI: 10.1007/s00248-021-01689-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/10/2021] [Indexed: 06/12/2023]
Abstract
Understanding temporal and spatial microbial community abundance and diversity variations is necessary to assess the functional roles played by microbial actors in the environment. In this study, we investigated spatial variability and temporal dynamics of two functional microbial sediment communities, methanogenic Archaea and methanotrophic bacteria, in Lake Bourget, France. Microbial communities were studied from 3 sites sampled 4 times over a year, with one core sampled at each site and date, and 5 sediment layers per core were considered. Microbial abundance in the sediment were determined using flow cytometry. Methanogens and methanotrophs community structures, diversity, and abundance were assessed using T-RFLP, sequencing, and real-time PCR targeting mcrA and pmoA genes, respectively. Changes both in structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics. Methanogen diversity was dominated by Methanomicrobiales (mainly Methanoregula) members, followed by Methanosarcinales and Methanobacteriales. For methanotrophs, diversity was dominated by Methylobacter in the deeper area and by Methylococcus in the shallow area. Organic matter appeared to be the main environmental parameter controlling methanogens, while oxygen availability influenced both the structure and abundance of the methanotrophic community.
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Affiliation(s)
- Emilie Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France.
| | - Elodie Billard
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
| | - Nathalie Tissot
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
| | - Stéphan Jacquet
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
| | - Isabelle Domaizon
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
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7
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Liu Q, Romani M, Wang J, Planer-Friedrich B, Pausch J, Dorodnikov M. Alternating Wet-Dry Cycles Rather than Sulfate Fertilization Control Pathways of Methanogenesis and Methane Turnover in Rice Straw-Amended Paddy Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:12075-12083. [PMID: 34409832 DOI: 10.1021/acs.est.1c03149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Alternate wet-drying (AWD) and sulfate fertilization have been considered as effective methods for lowering CH4 emissions from paddy soils. However, there is a clear knowledge gap between field studies that focus on the quantification of emissions and laboratory studies that investigate mechanisms. To elucidate mechanisms of CH4 production and oxidation under field conditions, rice was planted in straw-amended mesocosms with or without sulfate fertilization under continuously flooded conditions (FL) or two wet-dry cycles. CO2 and CH4 concentrations in soil air and their natural C isotope compositions were measured at stem elongation, booting, and flowering stages. CH4 concentration reached 51 mg C L-1 at the flowering stage under FL, while it decreased to 0.04 mg C L-1 under AWD. Relative 13C enrichment in CH4 and depletion in CO2 under AWD indicated CH4 oxidation. Ample organic substrate supply may have reduced competition between sulfate-reducing bacteria and methanogenic archaea, and therefore, it explains the absence of a decrease in CH4 concentrations in sulfate treatments. 13C enrichment in CO2 over time (6 and 7‰ with and without sulfate fertilizers, respectively) under FL indicates continuous contribution of hydrogenotrophic methanogenesis to CH4 production with ongoing rice growth. Overall, AWD could more efficiently reduce CH4 production than sulfate fertilization in rice straw-amended paddy soils.
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Affiliation(s)
- Qiong Liu
- Agroecology, BayCEER, University of Bayreuth, Bayreuth 95440, Germany
| | - Marco Romani
- Ente Nazionale Risi-Rice Research Centre, Castello d'Agogna 27030, Italy
| | - Jiajia Wang
- Environmental Geochemistry, BayCEER, University of Bayreuth, Bayreuth 95440, Germany
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | | | - Johanna Pausch
- Agroecology, BayCEER, University of Bayreuth, Bayreuth 95440, Germany
| | - Maxim Dorodnikov
- Soil Science of Temperate Ecosystems, Georg-August University of Göttingen, Göttingen 37077, Germany
- Biogeochemistry of Agroecosystems, Georg-August University of Göttingen, Göttingen 37077, Germany
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8
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Gontijo JB, Paula FS, Venturini AM, Yoshiura CA, Borges CD, Moura JMS, Bohannan BJM, Nüsslein K, Rodrigues JLM, Tsai SM. Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities. Mol Ecol 2021; 30:2560-2572. [PMID: 33817881 DOI: 10.1111/mec.15912] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 01/03/2023]
Abstract
The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH4 source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here, we report the in situ composition of CH4 cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH4 cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH4 emissions in the region.
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Affiliation(s)
- Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil.,Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Clovis D Borges
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - José Mauro S Moura
- Center for Interdisciplinary Formation, Federal University of Western Pará, Santarém, Brazil
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Jorge L Mazza Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
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9
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Shakoor A, Ashraf F, Shakoor S, Mustafa A, Rehman A, Altaf MM. Biogeochemical transformation of greenhouse gas emissions from terrestrial to atmospheric environment and potential feedback to climate forcing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:38513-38536. [PMID: 32770337 DOI: 10.1007/s11356-020-10151-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Carbon dioxide (CO2) is mainly universal greenhouse gas associated with climate change. However, beyond CO2, some other greenhouse gases (GHGs) like methane (CH4) and nitrous oxide (N2O), being two notable gases, contribute to global warming. Since 1900, the concentrations of CO2 and non-CO2 GHG emissions have been elevating, and due to the effects of the previous industrial revolution which is responsible for climate forcing. Globally, emissions of CO2, CH4, and N2O from agricultural sectors are increasing as around 1% annually. Moreover, deforestation also contributes 12-17% of total global GHGs. Perhaps, the average temperature is likely to increase globally, at least 2 °C by 2100-by mid-century. These circumstances are responsible for climate forcing, which is the source of various human health diseases and environmental risks. From agricultural soils, rhizospheric microbial communities have a significant role in the emissions of greenhouse gases. Every year, microbial communities release approximately 1.5-3 billion tons of carbon into the atmospheric environment. Microbial nitrification, denitrification, and respiration are the essential processes that affect the nitrogen cycle in the terrestrial environment. In the twenty-first century, climate change is the major threat faced by human beings. Climate change adversely influences human health to cause numerous diseases due to their direct association with climate change. This review highlights the different anthropogenic GHG emission sources, the response of microbial communities to climate change, climate forcing potential, and mitigation strategies through different agricultural management approaches and microbial communities.
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Affiliation(s)
- Awais Shakoor
- Department of Environment and Soil Sciences, University of Lleida, Avinguda Alcalde Rovira Roure 191, 25198, Lleida, Spain.
| | - Fatima Ashraf
- Department of Chemistry, Lahore College for Women University, Lahore, Pakistan
| | - Saba Shakoor
- Department of Zoology, The Women University Multan, Multan, Pakistan
| | - Adnan Mustafa
- National Engineering Laboratory for Improving Quality of Arable Land, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Abdul Rehman
- CAS-Key Laboratory of Crust-Mantle Materials and the Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Muhammad Mohsin Altaf
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Ecology and Environment, Hainan University, Haikou, 570228, People's Republic of China
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10
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Moterle DF, da Silva LS, Drescher GL, Müller EA. Relationship between soil solution electrochemical changes and methane and nitrous oxide emissions in different rice irrigation management systems. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:35591-35603. [PMID: 32594449 DOI: 10.1007/s11356-020-09744-7] [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: 01/28/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Rice (Oryza sativa L.) intermittent irrigation is a potential strategy to mitigate methane (CH4) and nitrous oxide (N2O) emissions, but the effects of dry-wetting intervals on soil electrochemical changes and plant characteristics should be considered. This study was conducted in a greenhouse evaluating CH4 and N2O fluxes in rice under five different irrigation management practices (continuous irrigation (CI), intermittent irrigation with flooding resumption in saturated soil condition (SSI) and soil moisture at field capacity (FCI), saturated soil and irrigation resumption with soil moisture bellow field capacity (FCS), and soil at field capacity (FCD)) and its relation to plant development and global warming potential (GWP). Soil electrochemical conditions and CH4 and N2O emissions were expressively affected by irrigation management. The CI system presented the greatest CH4 flux (20.14 g m-2) and GWP (462.7 g m-2 eq. CO2), whereas intermittent irrigation expressively reduced CH4 emissions. Overall, the N2O flux was low (bellow 20 μg m-2 h-1) even with N application, with greater emissions occurring at the FCD treatment at the beginning of the rice season. Soil moisture at field capacity had no CH4 flux but presented greater GWP (271 g m-2 eq. CO2) than intermittent irrigation systems due to N2O flux while compromising rice plant development. The best soil moisture condition to initiate a flooding cycle during intermittent irrigation is at saturated soil conditions.
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Affiliation(s)
- Diovane Freire Moterle
- Federal Institute of Education, Science and Technology of Rio Grande do Sul, 540 Osvaldo Aranha Ave, Bento Gonçalves, RS, 95700-000, Brazil
| | - Leandro Souza da Silva
- Department of Soil Science, Federal University of Santa Maria, 1000 Roraima Ave, Santa Maria, RS, 97105-900, Brazil.
| | - Gerson Laerson Drescher
- University of Arkansas System Division of Agriculture, 1366 West Altheimer Drive, Fayetteville, AR, 72704, USA
| | - Eduardo Augusto Müller
- Department of Soil Science, Federal University of Santa Maria, 1000 Roraima Ave, Santa Maria, RS, 97105-900, Brazil
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11
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Xu X, Zhang M, Xiong Y, Yuan J, Shaaban M, Zhou W, Hu R. The influence of soil temperature, methanogens and methanotrophs on methane emissions from cold waterlogged paddy fields. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 264:110421. [PMID: 32217313 DOI: 10.1016/j.jenvman.2020.110421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/25/2020] [Accepted: 03/07/2020] [Indexed: 06/10/2023]
Abstract
Paddy fields are major sources of atmospheric methane (CH4). However, CH4 emissions from cold-waterlogged paddy fields, a major type of paddy soil in China, remain unclear. Here we investigated the CH4 emissions and associated influential factors in cold-waterlogged paddy fields at two sites (Yangxin County and Daye City) in Hubei Province, South China. Normal paddy fields matched with parental material and cropping system were used as the controls. The CH4 emissions from cold-waterlogged fields were significantly higher than those from normal fields with (3.0-4.4-fold) or without (3.5-8.6-fold) rice. Rice planting increased CH4 emissions by 59-78% in cold-waterlogged fields and by 85-247% in normal fields. CH4 instantaneous fluxes were positively correlated with soil temperature and methanogen mcrA (methyl coenzyme M reductase alpha subunit) and methanotroph pmoA (methane monooxygenase) copy numbers at the annual scale. Under rice planting, mcrA copy number was higher in cold-waterlogged fields than in normal fields at both sites, whereas pmoA copy number had the same trend at the Daye site only. Soil temperature and water content influenced mcrA and pmoA copy numbers in the normal paddy fields, whereas soil organic matter content was more influential in the cold-waterlogged paddy fields. These findings suggest that perennial waterlogging is a prerequisite for substantial CH4 emissions from cold-waterlogged paddy fields, and it promotes the proliferation of methanogens and methanotrophs under rice planting. Therefore, CH4 production-oxidation processes are more active in cold-waterlogged paddy fields than in normal paddy fields.
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Affiliation(s)
- Xiangyu Xu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, PR China; Qianjiang Scientific Observing and Experimental Station of Agro-Environment and Arable Land Conservation, Ministry of Agriculture PR China, Qianjiang, 433100, China; Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China; Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Griculture, Wuhan, 430064, China
| | - Minmin Zhang
- Qianjiang Scientific Observing and Experimental Station of Agro-Environment and Arable Land Conservation, Ministry of Agriculture PR China, Qianjiang, 433100, China; Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China; Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Griculture, Wuhan, 430064, China
| | - Yousheng Xiong
- Qianjiang Scientific Observing and Experimental Station of Agro-Environment and Arable Land Conservation, Ministry of Agriculture PR China, Qianjiang, 433100, China; Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China; Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Griculture, Wuhan, 430064, China
| | - Jiafu Yuan
- Qianjiang Scientific Observing and Experimental Station of Agro-Environment and Arable Land Conservation, Ministry of Agriculture PR China, Qianjiang, 433100, China; Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China; Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Griculture, Wuhan, 430064, China
| | - Muhammad Shaaban
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Wei Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Ronggui Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, PR China.
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12
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Wang YQ, Xiao GQ, Cheng YY, Wang MX, Sun BY, Zhou ZF. The linkage between methane production activity and prokaryotic community structure in the soil within a shale gas field in China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:7453-7462. [PMID: 31884532 DOI: 10.1007/s11356-019-07454-3] [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: 06/29/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
Soil methane generation mainly driven by soil prokaryotic microbes can be coupled with the degradation of petroleum hydrocarbons (PHCs); however, the relationship between prokaryotic community structure and methane production activity in soil with the potential risk of PHC contamination is seldom reported. In this study, 3 soil samples (CS-1 to CS-3) in the area nearby an exploratory gas well and 5 soil samples (DC-1 to DC-5) in a drill cutting dump area were obtained from the Fuling shale gas field (Chongqing City, China). Then, the prokaryotic community structure was examined by Illumina Miseq sequencing, and the linkage between soil methane production rate (MPR) and prokaryotic community composition was analyzed. The results indicated that 2 samples (DC-4 and DC-5) collected from the drill cutting dump area had significantly higher MPR than the other samples, and a significant and positive relationship (r = 0.44, P < 0.05) was found between soil MPR and soil organic matter (OM) content. The prokaryotic community composition in the sample (DC-5) with the highest MPR was different from those in the other samples, and soil OM and MPR were the major factors significantly correlated with the prokaryotic community structure in this soil. The samples (DC-4 and DC-5) with higher MPR had a higher relative abundance of Archaea and different archaeal community structures from the other samples, and the MPR was the sole factor significantly correlated with the archaeal genus composition in this soil. Therefore, both the prokaryotic and archaeal community structures are essential in the determination of soil MPR, and the bacterial genus of Saccharibacteria and the archaeal genus of Methanolobus might be the key contributors for methane generation in this soil from the shale gas field.
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Affiliation(s)
- Yan-Qin Wang
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Guang-Quan Xiao
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Yong-Yi Cheng
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Ming-Xia Wang
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Bo-Ya Sun
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Zhi-Feng Zhou
- College of Resources and Environment, Southwest University, Chongqing, 400715, China.
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13
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Hao Q, Liu F, Zhang Y, Wang O, Xiao L. Methylobacter accounts for strong aerobic methane oxidation in the Yellow River Delta with characteristics of a methane sink during the dry season. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135383. [PMID: 31810682 DOI: 10.1016/j.scitotenv.2019.135383] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/03/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
Recent investigations demonstrate that some coastal wetlands are atmospheric methane sinks, but the regulatory mechanisms are not clear. Here, the main pathway and operator of methane oxidation in the Yellow River Delta (YRD) wetland, a methane source in the wet season but a methane sink in the dry season, were investigated. The anaerobic oxidation of methane (AOM) and aerobic methane oxidation (AMO) abilities of wetland soil were measured, and the microbial community structure was analyzed. The experimental results showed that AMO was active throughout the year. In contrast, AOM was weak and even undetected. The microbial community analysis indicated that Methylomicrobium and Methylobacter potentially scavenged methane in oxic environments. A representative strain of Methylobacter, which was isolated from the soil, presented a strong AMO ability at high concentrations of methane and air. Overall, this study showed that active AMO performing by Methylobacter may account for methane sink in the YRD wetland during the dry season. Our research not only has determined the way in which methane sinks are formed but also identified the potential functional microbes. In particular, we confirmed the function of potential methanotroph by pure culture. Our research provides biological evidence for why some wetlands have methane sink characteristics, which may help to understand the global methane change mechanism.
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Affiliation(s)
- Qinqin Hao
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Yuechao Zhang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Oumei Wang
- Binzhou Medical University, Yantai, 264003, PR China
| | - Leilei Xiao
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China.
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14
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Sun W, Sun X, Li B, Häggblom MM, Han F, Xiao E, Zhang M, Wang Q, Li F. Bacterial response to antimony and arsenic contamination in rice paddies during different flooding conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:273-285. [PMID: 31030134 DOI: 10.1016/j.scitotenv.2019.04.146] [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: 01/13/2019] [Revised: 03/31/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Rice is more vulnerable to arsenic (As) and antimony (Sb) contamination than other cereals due to the special cultivation methods, during which irrigation conditions are adjusted depending upon the growth stages. The changes in irrigation conditions may alter the oxidation states of Sb and As, which influences their mobility and bioavailability and hence uptake by rice. In this study, bacterial responses to As and Sb contamination in rice fields were investigated during two different stages of rice growth: the vegetative stage (flooded conditions), and the ripening stage (drained conditions). The substantial changes in the irrigation conditions caused a variation in geochemical parameters including the As- and Sb-extractable fractions. As and Sb were more mobile and bioaccessible during the flooded than under drained conditions. The microbial communities varied during two irrigation conditions, suggesting that the geochemical conditions may have different effects on the innate paddy microbiota. Therefore, various statistical tools including co-occurrence network and random forest (RF) were performed to reveal the environment-microbe interactions in two different irrigation conditions. One of the notable findings is that Sb- and As-related parameters exerted more influences during the flooded than under drained conditions. Furthermore, a detailed RF analysis indicated that the individual bacterial taxa may also respond differently to contaminant fractions during the two irrigation conditions. Notably, RF indicated that individual taxa such as Clostridiaceae and Geobacter may be responsible for biotransformation of As and Sb (e.g., As and Sb reduction). The results provided knowledge for As and Sb transformation during contrasting irrigation conditions and the potential mitigation strategy for contaminant removal.
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Affiliation(s)
- Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China.
| | - Xiaoxu Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Feng Han
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Enzong Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Miaomiao Zhang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Qi Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
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15
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Jiang Y, Qian H, Wang L, Feng J, Huang S, Hungate BA, van Kessel C, Horwath WR, Zhang X, Qin X, Li Y, Feng X, Zhang J, Deng A, Zheng C, Song Z, Hu S, van Groenigen KJ, Zhang W. Limited potential of harvest index improvement to reduce methane emissions from rice paddies. GLOBAL CHANGE BIOLOGY 2019; 25:686-698. [PMID: 30449058 DOI: 10.1111/gcb.14529] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/16/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Rice is a staple food for nearly half of the world's population, but rice paddies constitute a major source of anthropogenic CH4 emissions. Root exudates from growing rice plants are an important substrate for methane-producing microorganisms. Therefore, breeding efforts optimizing rice plant photosynthate allocation to grains, i.e., increasing harvest index (HI), are widely expected to reduce CH4 emissions with higher yield. Here we show, by combining a series of experiments, meta-analyses and an expert survey, that the potential of CH4 mitigation from rice paddies through HI improvement is in fact small. Whereas HI improvement reduced CH4 emissions under continuously flooded (CF) irrigation, it did not affect CH4 emissions in systems with intermittent irrigation (II). We estimate that future plant breeding efforts aimed at HI improvement to the theoretical maximum value will reduce CH4 emissions in CF systems by 4.4%. However, CF systems currently make up only a small fraction of the total rice growing area (i.e., 27% of the Chinese rice paddy area). Thus, to achieve substantial CH4 mitigation from rice agriculture, alternative plant breeding strategies may be needed, along with alternative management.
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Affiliation(s)
- Yu Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
- Institute of Applied Ecology, Nanjing Agricultural University, Nanjing, China
| | - Haoyu Qian
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Ling Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jinfei Feng
- China National Rice Research Institute, Hangzhou, China
| | - Shan Huang
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona
| | - Chris van Kessel
- Department of Plant Sciences, University of California, Davis, California
| | - William R Horwath
- Department of Land, Air & Water Resources, University of California, Davis, California
| | - Xingyue Zhang
- Department of Land, Air & Water Resources, University of California, Davis, California
| | - Xiaobo Qin
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Yue Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Xiaomin Feng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Jun Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Aixing Deng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Chenyan Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Zhenwei Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Shuijin Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina
| | | | - Weijian Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
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16
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Shi W, Pan G, Chen Q, Song L, Zhu L, Ji X. Hypoxia Remediation and Methane Emission Manipulation Using Surface Oxygen Nanobubbles. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8712-8717. [PMID: 30001132 DOI: 10.1021/acs.est.8b02320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Algal blooms in eutrophic waters often induce anoxia/hypoxia and enhance methane (CH4) emissions to the atmosphere, which may contribute to global warming. At present, there are very few strategies available to combat this problem. In this study, surface oxygen nanobubbles were tested as a novel approach for anoxia/hypoxia remediation and CH4 emission control. Incubation column experiments were conducted using sediment and water samples taken from Lake Taihu, China. The results indicated that algae-induced anoxia/hypoxia could be reduced or reversed after oxygen nanobubbles were loaded onto zeolite micropores and delivered to anoxic sediment. Cumulated CH4 emissions were also reduced by a factor of 3.2 compared to the control. This was mainly attributed to the manipulation of microbial processes using the surface oxygen nanobubbles, which potentially served as oxygen suppliers. The created oxygen-enriched environment simultaneously decreased methanogen but increased methanotroph abundances, making a greater fraction of organic carbon recycled as carbon dioxide (CO2) instead of CH4. The CH4/CO2 emission ratio decreased to 3.4 × 10-3 in the presence of oxygen nanobubbles, compared to 11 × 10-3 in the control, and therefore the global warming potential was reduced. This study proposes a possible strategy for anoxia/hypoxia remediation and CH4 emission control in algal bloom waters, which may benefit global warming mitigation.
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Affiliation(s)
- Wenqing Shi
- Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , China
- Center for Eco-Environment Research , Nanjing Hydraulic Research Institute , Nanjing 210098 , China
| | - Gang Pan
- Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , China
- School of Animal, Rural, and Environmental Sciences , Nottingham Trent University , Nottingham NG25 0QF , U.K
| | - Qiuwen Chen
- Center for Eco-Environment Research , Nanjing Hydraulic Research Institute , Nanjing 210098 , China
| | - Lirong Song
- Institute of Hydrobiology , Chinese Academy of Sciences , Wuhan 430075 , China
| | - Lin Zhu
- School of Environmental Science & Engineering , Nanjing University of Information Science & Technology , Nanjing 210044 , China
| | - Xiaonan Ji
- Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , China
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17
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Zhou B, Feng Y, Wang Y, Yang L, Xue L, Xing B. Impact of hydrochar on rice paddy CH 4 and N 2O emissions: A comparative study with pyrochar. CHEMOSPHERE 2018; 204:474-482. [PMID: 29679868 DOI: 10.1016/j.chemosphere.2018.04.056] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 02/22/2018] [Accepted: 04/11/2018] [Indexed: 06/08/2023]
Abstract
Hydrothermal carbonization (HTC) thermally converts wet biomasses to carbon materials, dramatically reducing energy use for drying and improving solid product yield compared to pyrolysis process. However, researches regarding agricultural usage of hydrochar (HC) are limited. In the present study, the influence of HC amendment on CH4 and N2O emissions, as well as global warming potential (GWP) and greenhouse gas intensity (GHGI) were investigated. Additionally, pyrochar (PC) treatments as well as two char-free control treatments with (CKU) or without (CK) N fertilizer were also included for comparison. Chars were produced from wheat straw (WC) and saw dust (SC) and applied at different rates (0.5% and 3%, w/w). Both hydrochar and pyrochar decreased paddy CH4 emissions when amended at a lower rate (0.5%) compared to CKU treatment, which was more obvious for pyrochar when applied at the rate of 3%. Contrarily, 3%-HC significantly stimulated CH4 emissions, which were around 5 and 3 times higher than that of CKU for WC and SC, respectively. Furthermore, hydrochar showed the potential to decrease paddy N2O emissions (6.06-32.32%) at both application rates. However, N2O emissions with PC treatments varied depending on application rate (20.20-75.76%). GWP and GHGI values of 0.5%-HC and PC treatments were similar, 6.67-25.00% and 3.85-25.00% lower than those of CKU treatment, respectively. However, 3%-HC amendments led to significantly increased GWP and GHGI. This study suggested that application rate of hydrochar used in rice fields should be taken into serious consideration to fulfill its potential in GHGs mitigation and minimize environmental side effects.
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Affiliation(s)
- Beibei Zhou
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Yanfang Feng
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, USA
| | - Yueman Wang
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Linzhang Yang
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng 224002, China
| | - Lihong Xue
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng 224002, China.
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, USA
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18
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Zhu L, Qin B, Zhou J, Van Dam B, Shi W. Effects of turbulence on carbon emission in shallow lakes. J Environ Sci (China) 2018; 69:166-172. [PMID: 29941252 DOI: 10.1016/j.jes.2017.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 06/08/2023]
Abstract
Turbulent mixing is enhanced in shallow lakes. As a result, exchanges across the air-water and sediment-water interfaces are increased, causing these systems to be large sources of greenhouse gases. This study investigated the effects of turbulence on carbon dioxide (CO2) and methane (CH4) emissions in shallow lakes using simulated mesocosm experiments. Results demonstrated that turbulence increased CO2 emissions, while simultaneously decreasing CH4 emissions by altering microbial processes. Under turbulent conditions, a greater fraction of organic carbon was recycled as CO2 instead of CH4, potentially reducing the net global warming effect because of the lower global warming potential of CO2 relative to CH4. The CH4/CO2 flux ratio was approximately 0.006 under turbulent conditions, but reached 0.078 in the control. The real-time quantitative PCR analysis indicated that methanogen abundance decreased and methanotroph abundance increased under turbulent conditions, inhibiting CH4 production and favoring the oxidation of CH4 to CO2. These findings suggest that turbulence may play an important role in the global carbon cycle by limiting CH4 emissions, thereby reducing the net global warming effect of shallow lakes.
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Affiliation(s)
- Lin Zhu
- Taihu Lake Laboratory Ecosystem Station, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, East Beijing Road 73, Nanjing 210008, China.
| | - Boqiang Qin
- Taihu Lake Laboratory Ecosystem Station, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, East Beijing Road 73, Nanjing 210008, China.
| | - Jian Zhou
- Taihu Lake Laboratory Ecosystem Station, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, East Beijing Road 73, Nanjing 210008, China
| | - Bryce Van Dam
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC, USA
| | - Wenqing Shi
- Center for Eco-Environmental Research, Nanjing Hydraulics Research Institute, Guangzhoulu 223, Nanjing 210029, China
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19
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Lyu Z, Lu Y. Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. ISME JOURNAL 2017; 12:411-423. [PMID: 29135970 PMCID: PMC5776455 DOI: 10.1038/ismej.2017.173] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/31/2017] [Accepted: 08/09/2017] [Indexed: 11/09/2022]
Abstract
Methanogens have long been considered strictly anaerobic and oxygen-sensitive microorganisms, but their ability to survive oxygen stress has also been documented. Indeed, methanogens have been found in oxidative environments, and antioxidant genes have been detected in their genomes. How methanogens adapt to oxidative environments, however, remain poorly understood. Here, we systematically predicted and annotated antioxidant features from representative genomes across six well-established methanogen orders. Based on functional gene content involved in production of reactive oxygen species, Hierarchical Clustering analyses grouped methanogens into two distinct clusters, corresponding to the Class I and II methanogens, respectively. Comparative genomics suggested a systematic shift in metabolisms across the two classes, resulting in an enrichment of antioxidant features in the Class II. Moreover, meta-analysis of 16 S rRNA gene sequences obtained from EnvDB indicated that members of Class II were more frequently recovered from microaerophilic and even oxic environments than the Class I members. Phylogenomic analysis suggested that the Class I and II methanogens might have evolved before and around the Great Oxygenation Event, respectively. The enrichment of antioxidant features in the Class II methanogens may have played a key role in the adaption of this group to oxidative environments today and historically.
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Affiliation(s)
- Zhe Lyu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, PR China.,Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Yahai Lu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, PR China.,College of Urban and Environmental Sciences, Peking University, Beijing, PR China
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20
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Kanaparthi D, Reim A, Martinson GO, Pommerenke B, Conrad R. Methane emission from feather moss stands. GLOBAL CHANGE BIOLOGY 2017; 23:4884-4895. [PMID: 28514080 DOI: 10.1111/gcb.13764] [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: 02/21/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
Data from remote sensing and Eddy towers indicate that forests are not always net sinks for atmospheric CH4 . However, studies describing specific sources within forests and functional analysis of microorganisms on sites with CH4 turnover are scarce. Feather moss stands were considered to be net sinks for carbon dioxide, but received little attention to their role in CH4 cycling. Therefore, we investigated methanogenic rates and pathways together with the methanogenic microbial community composition in feather moss stands from temperate and boreal forests. Potential rates of CH4 emission from intact moss stands (n = 60) under aerobic conditions ranged between 19 and 133 pmol CH4 h-1 gdw-1 . Temperature and water content positively influenced CH4 emission. Methanogenic potentials determined under N2 atmosphere in darkness ranged between 22 and 157 pmol CH4 h-1 gdw-1 . Methane production was strongly inhibited by bromoethane sulfonate or chloroform, showing that CH4 was of microbial origin. The moss samples tested contained fluorescent microbial cells and between 104 and 105 copies per gram dry weight moss of the mcrA gene coding for a subunit of the methyl CoM reductase. Archaeal 16S rRNA and mcrA gene sequences in the moss stands were characteristic for the archaeal families Methanobacteriaceae and Methanosarcinaceae. The potential methanogenic rates were similar in incubations with and without methyl fluoride, indicating that the CH4 was produced by the hydrogenotrophic rather than aceticlastic pathway. Consistently, the CH4 produced was depleted in 13 C in comparison with the moss biomass carbon and acetate accumulated to rather high concentrations (3-62 mM). The δ13 C of acetate was similar to that of the moss biomass, indicating acetate production by fermentation. Our study showed that the feather moss stands contained active methanogenic microbial communities producing CH4 by hydrogenotrophic methanogenesis and causing net emission of CH4 under ambient conditions, albeit at low rates.
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Affiliation(s)
- Dheeraj Kanaparthi
- Department of Biogeochemistry, Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
| | - Andreas Reim
- Department of Biogeochemistry, Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
| | - Guntars O Martinson
- Department of Biogeochemistry, Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
| | - Bianca Pommerenke
- Department of Biogeochemistry, Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
| | - Ralf Conrad
- Department of Biogeochemistry, Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
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Liu H, Wu X, Li Z, Wang Q, Liu D, Liu G. Responses of soil methanogens, methanotrophs, and methane fluxes to land-use conversion and fertilization in a hilly red soil region of southern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8731-8743. [PMID: 28213705 DOI: 10.1007/s11356-017-8628-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
Changes in land-uses and fertilization are important factors regulating methane (CH4) emissions from paddy soils. However, the responses of soil CH4 emissions to these factors and the underlying mechanisms remain unclear. The objective of this study was to explore the effects of land-use conversion from paddies to orchards and fertilization on soil CH4 fluxes, and the abundance and community compositions of methanogens and methanotrophs. Soil CH4 fluxes were quantified by static chamber and gas chromatography technology. Abundance and community structures of methanogens and methanotrophs (based on mcrA and pmoA genes, respectively) were determined by quantitative real-time PCR (qPCR), and terminal restriction fragment length polymorphism (TRFLP), cloning and sequence analysis, respectively. Results showed that land-use conversion from paddies to orchards dramatically decreased soil CH4 fluxes, whereas fertilization did not distinctly affect soil CH4 fluxes. Furthermore, abundance of methanogens and methanotrophs were decreased after converting paddies to orchards. Fertilization decreased the abundance of these microorganisms, but the values were not statistically significant. Moreover, land-use conversion had fatal effects on some members of the methanogenic archaea (Methanoregula and Methanosaeta), increased type II methanotrophs (Methylocystis and Methylosinus), and decreased type I methanotrophs (Methylobacter and Methylococcus). However, fertilization could only significantly affect type I methanotrophs in the orchard plots. In addition, CH4 fluxes from paddy soils were positively correlated with soil dissolved organic carbon contents and methanogens abundance, whereas CH4 fluxes in orchard plots were negatively related to methanotroph abundance. Therefore, our results suggested that land-use conversion from paddies to orchards could change the abundance and community compositions of methanogens and methanotrophs, and ultimately alter the soil CH4 fluxes. Overall, our study shed insight on the underlying mechanisms of how land-use conversion from paddies to orchards decreased CH4 emissions.
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Affiliation(s)
- Huifeng Liu
- 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 Science, Beijing, 100049, China
| | - Xing Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Joint Center for Global Change Studies, Beijing, 100875, China.
| | - Zongshan Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Joint Center for Global Change Studies, Beijing, 100875, China
| | - Qing Wang
- 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 Science, Beijing, 100049, China
| | - Dan Liu
- 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 Science, Beijing, 100049, China
| | - Guohua Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Joint Center for Global Change Studies, Beijing, 100875, China.
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22
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Wang W, Wu X, Chen A, Xie X, Wang Y, Yin C. Mitigating effects of ex situ application of rice straw on CH 4 and N 2O emissions from paddy-upland coexisting system. Sci Rep 2016; 6:37402. [PMID: 27869209 PMCID: PMC5116586 DOI: 10.1038/srep37402] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/28/2016] [Indexed: 11/22/2022] Open
Abstract
The in situ application of rice straw enhances CH4 emissions by a large margin. The ex situ application of rice straw in uplands, however, may mitigate total global warming potential (GWP) of CH4 and N2O emissions from paddy-upland coexisting systems. To evaluate the efficiency of this practice, two field trials were conducted in rice-rice-fallow and maize-rape cropping systems, respectively. Year-round measurements of CH4 and N2O emissions were conducted to evaluate the system-scaled GWP. The results showed that CH4 accounted for more than 98% of GWP in paddy. Straw removal from paddy decreased 44.7% (302.1 kg ha−1 yr−1) of CH4 emissions and 51.2% (0.31 kg ha−1 yr−1) of N2O emissions, thus decreased 44.8% (7693 kg CO2-eqv ha−1 yr−1) of annual GWP. N2O accounted for almost 100% of GWP in upland. Straw application in upland had insignificant effects on CH4 and N2O emissions, which increased GWP only by 91 kg CO2-eqv ha−1 yr−1. So, the transfer of straw from paddy to upland could decrease GWP by 7602 kg CO2-eqv ha−1 yr−1. Moreover, straw retention during late rice season contributed to 88.2% of annual GWP increment. It is recommended to transfer early rice straw to upland considering GWP mitigation, nutrient recycling and labor cost.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, Hunan, China
| | - Xiaohong Wu
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Anlei Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, Hunan, China
| | - Xiaoli Xie
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, Hunan, China
| | - Yunqiu Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, Hunan, China
| | - Chunmei Yin
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, Hunan, China
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Zhang J, Tang H, Zhu J, Lin X, Feng Y. Divergent responses of methanogenic archaeal communities in two rice cultivars to elevated ground-level O3. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 213:127-134. [PMID: 26895536 DOI: 10.1016/j.envpol.2016.01.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/02/2016] [Accepted: 01/21/2016] [Indexed: 05/20/2023]
Abstract
Inhibitive effect of elevated ground-level ozone (O3) on paddy methane (CH4) emission varies with rice cultivars. However, little information is available on its microbial mechanism. For this purpose, the responses of methane-metabolizing microorganisms, methanogenic archaea and methanotrophic bacteria to O3 pollution were investigated in the O3-tolerant (YD6) and the O3-sensitive (IIY084) cultivars at two rice growth stages in Free Air Concentration Elevation of O3 (O3-FACE) system of China. It was found that O3 pollution didn't change the abundances of Type I and Type II methanotrophic bacteria at two rice stages. For methanogenic archaea, their abundances in both cultivars were decreased by O3 pollution at the tillering stage. Furthermore, a greater negative influence on methanogenic archaeal community was observed on IIY084 than on YD6: at tillering stage, the alpha diversity indices of methanogenic archaeal community in IIY084 was decreased to a greater extent than in YD6; IIY084 shifted methanogenic archaeal community composition and decreased the abundances and the diversities of Methanosarcinaceae and Methanosaetaceae as well as the abundance of Methanomicrobiales, while the diversity of Methanocellaceae were increased in YD6. These findings indicate that the variations in the responses of paddy CH4 emission to O3 pollution between cultivars could result from the divergent responses of their methanogenic archaea.
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Affiliation(s)
- Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Haoye Tang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China.
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Pandit PS, Rahalkar MC, Dhakephalkar PK, Ranade DR, Pore S, Arora P, Kapse N. Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches. MICROBIAL ECOLOGY 2016; 71:634-644. [PMID: 26547567 DOI: 10.1007/s00248-015-0697-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Methanotrophs play a crucial role in filtering out methane from habitats, such as flooded rice fields. India has the largest area under rice cultivation in the world; however, to the best of our knowledge, methanotrophs have not been isolated and characterized from Indian rice fields. A cultivation strategy composing of a modified medium, longer incubation time, and serial dilutions in microtiter plates was used to cultivate methanotrophs from a rice rhizosphere sample from a flooded rice field in Western India. We compared the cultured members with the uncultured community as revealed by three culture-independent methods. A novel type Ia methanotroph (Sn10-6), at the rank of a genus, and a putative novel species of a type II methanotroph (Sn-Cys) were cultivated from the terminal positive dilution (10(-6)). From lower dilution (10(-4)), a strain of Methylomonas spp. was cultivated. All the three culture-independent analyses, i.e., pmoA clone library, terminal restriction fragment length polymorphism (T-RFLP), and metagenomics approach, revealed the dominance of type I methanotrophs. Only metagenomic analysis showed significant presence of type II methanotrophs, albeit in lower proportion (37 %). All the three isolates showed relevance to the methanotrophic community as depicted by uncultured methods; however, the cultivated members might not be the most dominant ones. In conclusion, a combined cultivation and cultivation-independent strategy yielded us a broader picture of the methanotrophic community from rice rhizospheres of a flooded rice field in India.
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Affiliation(s)
- Pranitha S Pandit
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Monali C Rahalkar
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
| | | | - Dilip R Ranade
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Microbial Culture Collection, NCCS, Sai-Trinity Building Garware Circle, Pashan, Pune, Maharashtra, 411021, India
| | - Soham Pore
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Preeti Arora
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Neelam Kapse
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
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25
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Breidenbach B, Blaser MB, Klose M, Conrad R. Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community. Environ Microbiol 2015; 18:2868-85. [PMID: 26337675 DOI: 10.1111/1462-2920.13041] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 11/27/2022]
Abstract
Crop rotation of flooded rice with upland crops is a common management scheme allowing the reduction of water consumption along with the reduction of methane emission. The introduction of an upland crop into the paddy rice ecosystem leads to dramatic changes in field conditions (oxygen availability, redox conditions). However, the impact of this practice on the archaeal and bacterial communities has scarcely been studied. Here, we provide a comprehensive study focusing on the crop rotation between flooded rice in the wet season and upland maize (RM) in the dry season in comparison with flooded rice (RR) in both seasons. The composition of the resident and active microbial communities was assessed by 454 pyrosequencing targeting the archaeal and bacterial 16S rRNA gene and 16S rRNA. The archaeal community composition changed dramatically in the rotational fields indicated by a decrease of anaerobic methanogenic lineages and an increase of aerobic Thaumarchaeota. Members of Methanomicrobiales, Methanosarcinaceae, Methanosaetaceae and Methanocellaceae were equally suppressed in the rotational fields indicating influence on both acetoclastic and hydrogenotrophic methanogens. On the contrary, members of soil crenarchaeotic group, mainly Candidatus Nitrososphaera, were higher in the rotational fields, possibly indicating increasing importance of ammonia oxidation during drainage. In contrast, minor effects on the bacterial community were observed. Acidobacteria and Anaeromyxobacter spp. were enriched in the rotational fields, whereas members of anaerobic Chloroflexi and sulfate-reducing members of Deltaproteobacteria were found in higher abundance in the rice fields. Combining quantitative polymerase chain reaction and pyrosequencing data revealed increased ribosomal numbers per cell for methanogenic species during crop rotation. This stress response, however, did not allow the methanogenic community to recover in the rotational fields during re-flooding and rice cultivation. In summary, the analyses showed that crop rotation with upland maize led to dramatic changes in the archaeal community composition whereas the bacterial community was only little affected.
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Affiliation(s)
| | - Martin B Blaser
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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26
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Leng L, Chang J, Geng K, Lu Y, Ma K. Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate. MICROBIAL ECOLOGY 2015; 70:88-96. [PMID: 25475784 DOI: 10.1007/s00248-014-0540-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 11/21/2014] [Indexed: 06/04/2023]
Abstract
Methanotrophs are crucial in regulating methane emission from rice field systems. Type II methanotrophs in particular are often observed in high abundance in paddy soil. Some cultivated species of Methylocystis are able to grow on acetate in the absence of methane. We hypothesize that the dominant type II methanotrophs in paddy soil might facultatively utilize acetate for growth, which we evaluate in the present study. The measurement of methane oxidation rates showed that the methanotrophic activity in paddy soil was inhibited by the addition of acetate compared to the continuous supplementation of methane, but the paddy soil maintained the methane oxidation capacity and recovered following methane supplementation. Terminal restriction fragment length polymorphism analysis (T-RFLP) combined with cloning and sequencing of pmoA genes showed that Methylocystis was enriched after incubation with added acetate, while the type I methanotrophs Methylocaldum/Methylococcus and Methylobacter were enriched by methane supplementation. A comparison of pmoA sequences obtained in this study with those in the public database indicated that they were globally widespread in paddy soils or in associated with rice roots. Furthermore, we performed stable isotope probing (SIP) of pmoA messenger RNA (mRNA) to investigate the assimilation of (13)C-acetate by paddy soil methanotrophs. RNA-SIP revealed that Methylocystis-related methanotrophs which shared the same genotype of the above enriched species were significantly labelled. It indicates that these methanotrophs actively assimilated the labelled acetate in paddy soil. Altogether, these results suggested that uncultivated Methylocystis species are facultative methanotrophs utilizing acetate as a secondary carbon source in paddy soil.
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Affiliation(s)
- Lingqin Leng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
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27
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Lee HJ, Jeong SE, Kim PJ, Madsen EL, Jeon CO. High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy. Front Microbiol 2015; 6:639. [PMID: 26161079 PMCID: PMC4479796 DOI: 10.3389/fmicb.2015.00639] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/12/2015] [Indexed: 11/24/2022] Open
Abstract
The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations decreased sharply to below detection limits at 8 mm depth. Pyrosequencing of 16S rRNA genes showed that bacterial and archaeal communities varied according to the oxic, oxic-anoxic, and anoxic zones, indicating that oxygen is a determining factor for the distribution of bacterial and archaeal communities. Aerobic methanotrophs were maximally observed near the oxic-anoxic interface, while methane, TOC, and methanogens were highest in the rhizosphere soil at 30–200 mm depth, suggesting that methane is produced mainly from organic carbon derived from rice plants and is metabolized aerobically. The relative abundances of type I methanotrophs such as Methylococcus, Methylomonas, and Methylocaldum decreased more drastically than those of type II methanotrophs (such as Methylocystis and Methylosinus) with increasing depth. Methanosaeta and Methanoregula were predominant methanogens at all depths, and the relative abundances of Methanosaeta, Methanoregula, and Methanosphaerula, and GOM_Arc_I increased with increasing depth. Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface), we have identified populations of methanogens (Methanosaeta, Methanoregula, Methanocella, Methanobacterium, and Methanosphaerula), and methanotrophs (Methylosarcina, Methylococcus, Methylosinus, and unclassified Methylocystaceae) that are likely physiologically active in situ.
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Affiliation(s)
- Hyo Jung Lee
- Department of Life Science, Chung-Ang University Seoul, South Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University Seoul, South Korea
| | - Pil Joo Kim
- Division of Applied Life Science, Gyeongsang National University Jinju, South Korea
| | - Eugene L Madsen
- Department of Microbiology, Cornell University Ithaca, NY, USA
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University Seoul, South Korea
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28
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Liu D, Ishikawa H, Nishida M, Tsuchiya K, Takahashi T, Kimura M, Asakawa S. Effect of paddy-upland rotation on methanogenic archaeal community structure in paddy field soil. MICROBIAL ECOLOGY 2015; 69:160-168. [PMID: 25113614 DOI: 10.1007/s00248-014-0477-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/31/2014] [Indexed: 06/03/2023]
Abstract
Methanogenic archaea are strict anaerobes and demand highly reduced conditions to produce methane in paddy field soil. However, methanogenic archaea survive well under upland and aerated conditions in paddy fields and exhibit stable community. In the present study, methanogenic archaeal community was investigated in fields where paddy rice (Oryza sativa L.) under flooded conditions was rotated with soybean (Glycine max [L.] Merr.) under upland conditions at different rotation histories, by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR methods targeting 16S rRNA and mcrA genes, respectively. Soil samples collected from the fields before flooding or seeding, during crop cultivation and after harvest of crops were analyzed. The abundance of the methanogenic archaeal populations decreased to about one-tenth in the rotational plots than in the consecutive paddy (control) plots. The composition of the methanogenic archaeal community also changed. Most members of the methanogenic archaea consisting of the orders Methanosarcinales, Methanocellales, Methanomicrobiales, and Methanobacteriales existed autochthonously in both the control and rotational plots, while some were strongly affected in the rotational plots, with fatal effect to some members belonging to the Methanosarcinales. This study revealed that the upland conversion for one or longer than 1 year in the rotational system affected the methanogenic archaeal community structure and was fatal to some members of methanogenic archaea in paddy field soil.
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Affiliation(s)
- Dongyan Liu
- Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi, 464-8601, Japan,
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29
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Franchini AG, Henneberger R, Aeppli M, Zeyer J. Methane dynamics in an alpine fen: a field-based study on methanogenic and methanotrophic microbial communities. FEMS Microbiol Ecol 2014; 91:fiu032. [PMID: 25789997 DOI: 10.1093/femsec/fiu032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Wetlands are important sources of the greenhouse gas methane (CH4). We provide an in situ study of CH4 dynamics in the permanently submerged soil of a Swiss alpine fen. Physico-chemical pore water analyses were combined with structural and microbiological analyses of soil cores at high vertical resolution down to 50 cm depth. Methanotrophs and methanogens were active throughout the depth profile, and highest abundance of active methanotrophs and methanogens [6.1 × 10(5) and 1.1 × 10(7) pmoA and mcrA transcripts (g soil)(-1), respectively] was detected in the uppermost 2 cm of the soil. Active methanotrophic communities in the near-surface zone, dominated by viable mosses, varied from the communities in the deeper zones, but further changes with depth were not pronounced. Apart from a distinct active methanogenic community in the uppermost sample, a decrease of acetoclastic Methanosaetaceae with depth was observed in concomitance with decreasing root surface area. Overall, root surface area correlated with mcrA transcript abundance and CH4 pore water concentrations, which peaked (137.1 μM) at 10 to 15 cm depth. Our results suggest that stimulation of methanogenesis by root exudates of vascular plants had a stronger influence on CH4 dynamics than stimulation of CH4 oxidation by O2 input.
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Affiliation(s)
- Alessandro G Franchini
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Meret Aeppli
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Josef Zeyer
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
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30
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Chen R, Wang Y, Wei S, Wang W, Lin X. Windrow composting mitigated CH4emissions: characterization of methanogenic and methanotrophic communities in manure management. FEMS Microbiol Ecol 2014; 90:575-86. [DOI: 10.1111/1574-6941.12417] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/11/2014] [Accepted: 08/13/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ruirui Chen
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
| | - Yiming Wang
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
| | - Shiping Wei
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
| | - Wei Wang
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
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31
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Ahn JH, Choi MY, Kim BY, Lee JS, Song J, Kim GY, Weon HY. Effects of water-saving irrigation on emissions of greenhouse gases and prokaryotic communities in rice paddy soil. MICROBIAL ECOLOGY 2014; 68:271-283. [PMID: 24682309 DOI: 10.1007/s00248-014-0371-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 01/15/2014] [Indexed: 06/03/2023]
Abstract
The effects of water-saving irrigation on emissions of greenhouse gases and soil prokaryotic communities were investigated in an experimental rice field. The water layer was kept at 1-2 cm in the water-saving (WS) irrigation treatment and at 6 cm in the continuous flooding (CF) irrigation treatment. WS irrigation decreased CH(4) emissions by 78 % and increased N(2)O emissions by 533 %, resulting in 78 % reduction of global warming potential compared to the CF irrigation. WS irrigation did not affect the abundance or phylogenetic distribution of bacterial/archaeal 16S rRNA genes and the abundance of bacterial/archaeal 16S rRNAs. The transcript abundance of CH(4) emission-related genes generally followed CH(4) emission patterns, but the difference in abundance between mcrA transcripts and amoA/pmoA transcripts best described the differences in CH(4) emissions between the two irrigation practices. WS irrigation increased the relative abundance of 16S rRNAs and functional gene transcripts associated with Anaeromyxobacter and Methylocystis spp., suggesting that their activities might be important in emissions of the greenhouse gases. The N(2)O emission patterns were not reflected in the abundance of N(2)O emission-related genes and transcripts. We showed that the alternative irrigation practice was effective for mitigating greenhouse gas emissions from rice fields and that it did not affect the overall size and structure of the soil prokaryotic community but did affect the activity of some groups.
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Affiliation(s)
- Jae-Hyung Ahn
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707, Republic of Korea
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Ahn JH, Choi MY, Lee HW, Kim BY, Song J, Kim MS, Weon HY. Analysis of Community Structure of Metabolically Active Bacteria in a Rice Field Subjected to Long-Term Fertilization Practices. ACTA ACUST UNITED AC 2013. [DOI: 10.7745/kjssf.2013.46.6.585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Methanogenic pathway and fraction of CH(4) oxidized in paddy fields: seasonal variation and effect of water management in winter fallow season. PLoS One 2013; 8:e73982. [PMID: 24069259 PMCID: PMC3771911 DOI: 10.1371/journal.pone.0073982] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 07/25/2013] [Indexed: 11/26/2022] Open
Abstract
A 2-year field and incubation experiment was conducted to investigate δ13C during the processes of CH4 emission from the fields subjected to two water managements (flooding and drainage) in the winter fallow season, and further to estimate relative contribution of acetate to total methanogenesis (Fac) and fraction of CH4 oxidized (Fox) based on the isotopic data. Compared with flooding, drainage generally caused CH4, either anaerobically or aerobically produced, depleted in 13C. There was no obvious difference between the two in transport fractionation factor (εtransport) and δ13C-value of emitted CH4. CH4 emission was negatively related to its δ13C-value in seasonal variation (P<0.01). Acetate-dependent methanogenesis in soil was dominant (60–70%) in the late season, while drainage decreased Fac-value by 5–10%. On roots however, CH4 was mostly produced through H2/CO2 reduction (60–100%) over the season. CH4 oxidation mainly occurred in the first half of the season and roughly 10–90% of the CH4 was oxidized in the rhizosphere. Drainage increased Fox-value by 5–15%, which is possibly attributed to a significant decrease in production while no simultaneous decrease in oxidation. Around 30–70% of the CH4 was oxidized at the soil-water interface when CH4 in pore water was released into floodwater, although the amount of CH4 oxidized therein might be negligible relative to that in the rhizosphere. CH4 oxidation was also more important in the first half of the season in lab conditions and about 5–50% of the CH4 was oxidized in soil while almost 100% on roots. Drainage decreased Fox-value on roots by 15% as their CH4 oxidation potential was highly reduced. The findings suggest that water management in the winter fallow season substantially affects Fac in the soil and Fox in the rhizosphere and roots rather than Fac on roots and Fox at the soil-water interface.
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Lüke C, Frenzel P, Ho A, Fiantis D, Schad P, Schneider B, Schwark L, Utami SR. Macroecology of methane-oxidizing bacteria: the β-diversity ofpmoAgenotypes in tropical and subtropical rice paddies. Environ Microbiol 2013; 16:72-83. [DOI: 10.1111/1462-2920.12190] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claudia Lüke
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
- Radboud University Nijmegen; Heyendaalsweg 135 Nijmegen 6525 AJ The Netherlands
| | - Peter Frenzel
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
| | - Adrian Ho
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
- Laboratory for Microbial Ecology and Technology (LabMET); Faculty of Bioscience Engineering; Coupure Links 653 Ghent 9000 Belgium
| | - Dian Fiantis
- Department of Soil Science; Faculty of Agriculture; Andalas University; Kampus Unand Limau Manis Padang 25163 Indonesia
| | - Peter Schad
- Department Ecology and Ecosystem Management; Center of Life and Food Sciences Weihenstephan; Technische Universität München; Lehrstuhl für Bodenkunde Freising-Weihenstephan D-85350 Germany
| | - Bellinda Schneider
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
| | - Lorenz Schwark
- Institute of Geosciences; University Kiel; Ludewig-Meyn-Straße 10 Kiel 24118 Germany
- WA-OIGC; Curtin University; Perth WA 6845 Australia
| | - Sri Rahayu Utami
- Department of Soil Science; Faculty of Agriculture; Brawijaya University; Jalan Veteran Malang 65145 East Java Indonesia
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Dry/Wet cycles change the activity and population dynamics of methanotrophs in rice field soil. Appl Environ Microbiol 2013; 79:4932-9. [PMID: 23770899 DOI: 10.1128/aem.00850-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (using terminal restriction fragment length polymorphism [T-RFLP]), and abundance (using quantitative PCR [qPCR]) of methanotroph pmoA genes (encoding a subunit of particulate methane monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA were relatively low but were significantly stimulated by drainage. In contrast, however, in the rhizosphere and surface soils, potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (and to a lesser extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded conditions. Drainage affected the composition of the methanotrophic community only minimally but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in the abundance, composition, and activity of the various type I and type II methanotrophs on both a seasonal and a spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced the attenuation of methane flux into the atmosphere.
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Li X, Wang H, Gan S, Jiang D, Tian G, Zhang Z. Eco-stoichiometric alterations in paddy soil ecosystem driven by phosphorus application. PLoS One 2013; 8:e61141. [PMID: 23667435 PMCID: PMC3646879 DOI: 10.1371/journal.pone.0061141] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 03/06/2013] [Indexed: 12/02/2022] Open
Abstract
Agricultural fertilization may change processes of elemental biogeochemical cycles and alter the ecological function. Ecoenzymatic stoichiometric feature plays a critical role in global soil carbon (C) metabolism, driving element cycles, and mediating atmospheric composition in response to agricultural nutrient management. Despite the importance on crop growth, the role of phosphorous (P) in compliance with eco-stoichiometry on soil C and nitrogen (N) sequestration in the paddy field remains poorly understood in the context of climate change. Here, we collected soil samples from a field experiment after 6 years of chemical P application at a gradient of 0 (P-0), 30 (P-30), 60 (P-60), and 90 (P-90) kg ha−1 in order to evaluate the role of P on stoichiometric properties in terms of soil chemical, microbial biomass, and eco-enzyme activities as well as greenhouse gas (GHG: CO2, N2O and CH4) emissions. Continuous P input increased soil total organic C and N by 1.3–9.2% and 3%–13%, respectively. P input induced C and N limitations as indicated by the decreased ratio of C:P and N:P in the soil and microbial biomass. A synergistic mechanism among the ecoenzymatic stoichiometry, which regulated the ecological function of microbial C and N acquisition and were stoichiometrically related to P input, stimulated soil C and N sequestration in the paddy field. The lower emissions of N2O and CH4 under the higher P application (P-60 and P-90) in July and the insignificant difference in N2O emission in August compared to P-30; however, continuous P input enhanced CO2 fluxes for both samplings. There is a technical conflict for simultaneously regulating three types of GHGs in terms of the eco-stoichiometry mechanism under P fertilization. Thus, it is recommended that the P input in paddy fields not exceed 60 kg ha−1 may maximize soil C sequestration, minimize P export, and guarantee grain yields.
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Affiliation(s)
- Xia Li
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Hang Wang
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - ShaoHua Gan
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - DaQian Jiang
- Department of Earth and Environmental Engineering, Columbia University, New York, New York, United States of America
| | - GuangMing Tian
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - ZhiJian Zhang
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
- Department of Earth and Environmental Engineering, Columbia University, New York, New York, United States of America
- China Academy of West Region Development, Zhejiang University, Hangzhou, China
- * E-mail:
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Xu Y, Ma K, Huang S, Liu L, Lu Y. Diel cycle of methanogen mcrA transcripts in rice rhizosphere. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:655-663. [PMID: 23760937 DOI: 10.1111/j.1758-2229.2012.00392.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/01/2012] [Indexed: 06/02/2023]
Abstract
Methanogens are known to inhabit not only the anaerobic bulk soil but also the rhizosphere of rice plants. The release of root exudates, a major carbon source for CH4 production in the rhizosphere, is closely coupled to plant photosynthesis. In the present study we hypothesized that the diel cycle of plant photosynthetic activity may shape the structure and function of methanogens in the rhizosphere of rice. We performed a field experiment to determine the diel dynamics of methanogen mcrA and their transcripts in the rhizosphere and bulk soil. The chemistry of NH4 (+) , NO3 (-) , SO4 (2-) and Fe(II) in the rice rhizosphere remained constant over a diel sampling. The mcrA copy number and their transcripts were greater in the rice rhizosphere compared with the bulk soil, indicating the enhanced activity of methanogens in the rhizosphere. The hydrogenotrophic Methanomicrobiales in particular increased in the rhizosphere whereas Methanosarcinaceae were more abundant in the bulk soil. Both the phylogenetic affiliation and copy numbers of methanogen mcrA in the rice rhizosphere did not display diel dynamics. The mcrA transcripts, however, significantly increased in the night compared with the daytime. The diel pattern of physical factors like temperature appeared not to affect the methanogen dynamics. The response of mcrA transcripts is probably due to the plant attributes, which release less O2 from roots in the night and hence stimulate the methanogen gene transcription and activity compared with the daytime.
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Affiliation(s)
- Yuan Xu
- College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, China
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Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. Appl Environ Microbiol 2011; 78:445-54. [PMID: 22101043 DOI: 10.1128/aem.06934-11] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Intermittent drainage can substantially reduce methane emission from rice fields, but the microbial mechanisms remain poorly understood. In the present study, we determined the rates of methane production and emission, the dynamics of ferric iron and sulfate, and the abundance of methanogen mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase) and their transcripts in response to alternate dry/wet cycles in paddy field soil. We found that intermittent drainage did not affect the growth of rice plants but significantly reduced the rates of both methane production and emission. The dry/wet cycles also resulted in shifts of soil redox conditions, increasing the concentrations of ferric iron and sulfate in the soil. Quantitative PCR analysis revealed that both mcrA gene copies and mcrA transcripts significantly decreased after dry/wet alternation compared to continuous flooding. Correlation and regression analyses showed that the abundance of mcrA genes and transcripts positively correlated with methane production potential and soil water content and negatively correlated with the concentrations of ferric iron and sulfate in the soil. However, the transcription of mcrA genes was reduced to a greater extent than the abundance of mcrA genes, resulting in very low mcrA transcript/gene ratios after intermittent drainage. Furthermore, terminal restriction fragment length polymorphism analysis revealed that the composition of methanogenic community remained stable under dry/wet cycles, whereas that of metabolically active methanogens strongly changed. Collectively, our study demonstrated a stronger effect of intermittent drainage on the abundance of mcrA transcripts than of mcrA genes in rice field soil.
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Angel R, Claus P, Conrad R. Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME JOURNAL 2011. [PMID: 22071343 DOI: 10.1038/ismej.2011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The prototypical representatives of the Euryarchaeota--the methanogens--are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. However, we found methanogens of the genera Methanosarcina and Methanocella to be present in many types of upland soils (including dryland soils) sampled globally. These methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any additional carbon source. Analysis of the archaeal 16S ribosomal RNA gene community profile in the incubated samples through terminal restriction fragment length polymorphism and quantification through quantitative PCR indicated dominance of Methanosarcina, whose gene copy numbers also correlated with methane production rates. Analysis of the δ(13)C of the methane further supported this, as the dominant methanogenic pathway was in most cases aceticlastic, which Methanocella cannot perform. Sequences of the key methanogenic enzyme methyl coenzyme M reductase retrieved from the soil samples before incubation confirmed that Methanosarcina and Methanocella are the dominant methanogens, though some sequences of Methanobrevibacter and Methanobacterium were also detected. The global occurrence of only two active methanogenic archaea supports the hypothesis that these are autochthonous members of the upland soil biome and are well adapted to their environment.
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Affiliation(s)
- Roey Angel
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Angel R, Claus P, Conrad R. Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME JOURNAL 2011; 6:847-62. [PMID: 22071343 DOI: 10.1038/ismej.2011.141] [Citation(s) in RCA: 212] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The prototypical representatives of the Euryarchaeota--the methanogens--are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. However, we found methanogens of the genera Methanosarcina and Methanocella to be present in many types of upland soils (including dryland soils) sampled globally. These methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any additional carbon source. Analysis of the archaeal 16S ribosomal RNA gene community profile in the incubated samples through terminal restriction fragment length polymorphism and quantification through quantitative PCR indicated dominance of Methanosarcina, whose gene copy numbers also correlated with methane production rates. Analysis of the δ(13)C of the methane further supported this, as the dominant methanogenic pathway was in most cases aceticlastic, which Methanocella cannot perform. Sequences of the key methanogenic enzyme methyl coenzyme M reductase retrieved from the soil samples before incubation confirmed that Methanosarcina and Methanocella are the dominant methanogens, though some sequences of Methanobrevibacter and Methanobacterium were also detected. The global occurrence of only two active methanogenic archaea supports the hypothesis that these are autochthonous members of the upland soil biome and are well adapted to their environment.
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Affiliation(s)
- Roey Angel
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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