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Harada M, Endo A, Wada S, Watanabe T, Epron D, Asakawa S. Ubiquity of methanogenic archaea in the trunk of coniferous and broadleaved tree species in a mountain forest. Antonie Van Leeuwenhoek 2024; 117:107. [PMID: 39060562 DOI: 10.1007/s10482-024-02004-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, Cryptomeria japonica, Quercus crispula, Fraxinus mandshurica, Acer pictum, Aesculus turbinata, Magnolia obovata, and Populus tremula. Amplicon sequencing analysis of 16S rRNA genes showed that Methanobacteriaceae predominated the archaeal communities and Methanomassiliicoccaceae also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal mcrA genes from all the tree species, with a maximum of 107 copies g-1 dry wood. Digital PCR analysis also detected mcrA genes derived from Methanobacterium spp. and Methanobrevibacter spp. from several samples, with a maximum of 105 and 104 copies g-1 dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 106 cells g-1 dry wood was enumerated from a heartwood sample of C. japonica. Methanogenic archaea related to Methanobacterium beijingense were cultivated from a heartwood sample of Q. crispula and F. mandshurica. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems.
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Affiliation(s)
- Mikitoshi Harada
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Atsuya Endo
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Shuji Wada
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Takeshi Watanabe
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.
| | - Daniel Epron
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Susumu Asakawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
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Li Q, Deng H, He R, Hu S, Sun L, Li M, Wu QL, Zeng J. Effects of different emergent macrophytes on methane flux and rhizosphere microbial communities in wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172565. [PMID: 38642750 DOI: 10.1016/j.scitotenv.2024.172565] [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: 09/29/2023] [Revised: 03/02/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
Emergent macrophytes are of great importance for the structure and functioning of wetland ecosystems and play a significant role in environmental improvement, element cycling, and greenhouse gas (GHG) emissions. However, our understanding of how GHG fluxes differ among macrophyte species and its links with the microbial communities remain limited. In this study, we investigated the rhizosphere microbial communities (including total bacteria, methanotrophs, and methanogens) and the GHG fluxes associated with four emergent macrophytes-Phragmites australis, Thalia dealbata, Pontederia cordata, and Zizania latifolia-collected from Xuanwu Lake wetland, China. We observed the highest CH4 flux (FCH4) (9.35 ± 2.52 mg·m-2·h-1) from Z. latifolia zone, followed by P. australis, P. cordata, and T. dealbata zones (5.38 ± 1.63, 2.38 ± 2.91, and 2.02 ± 0.69 mg·m-2·h-1, respectively). Methanogenesis was methylotrophic at all sites, as the 13C-CH4 values were higher than -64 ‰ and the fractionation coefficients were lower than 1.055. We found a positive linear relationship between FCH4 and the methanogen community, in particular the relative abundances of Methanobacterium and Methanosarcina, indicating that the variations in FCH4 among the studied macrophyte-dominated zones might be attributed to the differences in rhizosphere microbial communities. The methane emissions in various macrophyte zones might be due to the higher capacity of methanogenesis compared to methane oxidation which was inhibited by nutrient-rich sediments. Our findings provide insights for selecting specific emergent macrophytes characterized by low FCH4 in wetland ecological restoration.
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Affiliation(s)
- Qisheng Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyang Deng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rujia He
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Siwen Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Lijie Sun
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Mengyuan Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China; Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiujiang 332899, China.
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Pereira-Mora L, Guerrero LD, Erijman L, Fernández-Scavino A. Tartrate fermentation with H 2 production by a new member of Sporomusaceae enriched from rice paddy soil. Appl Environ Microbiol 2024; 90:e0235123. [PMID: 38517167 PMCID: PMC11026083 DOI: 10.1128/aem.02351-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/03/2024] [Indexed: 03/23/2024] Open
Abstract
In rice paddies, soil and plant-derived organic matter are degraded anaerobically to methane (CH4), a powerful greenhouse gas. The highest rate of methane emission occurs during the reproductive stage of the plant when mostly dicarboxylic acids are exudated by the roots. The emission of methane at this stage depends largely on the cooperative interaction between dicarboxylic acid-fermenting bacteria and methanogenic archaea in the rhizosphere. The fermentation of tartrate, one of the major acids exudated, has been scarcely explored in rice paddy soils. In this work, we characterized an anaerobic consortium from rice paddy soil composed of four bacterial strains, whose principal member (LT8) can ferment tartrate, producing H2 and acetate. Tartrate fermentation was accelerated by co-inoculation with a hydrogenotrophic methanogen. The assembled genome of LT8 possesses a Na+-dependent oxaloacetate decarboxylase and shows that this bacterium likely invests part of the H2 produced to reduce NAD(P)+ to assimilate C from tartrate. The phylogenetic analysis of the 16S rRNA gene, the genome-based classification as well as the average amino acid identity (AAI) indicated that LT8 belongs to a new genus within the Sporomusaceae family. LT8 shares a few common features with its closest relatives, for which tartrate degradation has not been described. LT8 is limited to a few environments but is more common in rice paddy soils, where it might contribute to methane emissions from root exudates.IMPORTANCEThis is the first report of the metabolic characterization of a new anaerobic bacterium able to degrade tartrate, a compound frequently associated with plants, but rare as a microbial metabolite. Tartrate fermentation by this bacterium can be coupled to methanogenesis in the rice rhizosphere where tartrate is mainly produced at the reproductive stage of the plant, when the maximum methane rate emission occurs. The interaction between secondary fermentative bacteria, such as LT8, and methanogens could represent a fundamental step in exploring mitigation strategies for methane emissions from rice fields. Possible strategies could include controlling the activity of these secondary fermentative bacteria or selecting plants whose exudates are more difficult to ferment.
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Affiliation(s)
- Luciana Pereira-Mora
- Laboratorio de Ecología Microbiana y Microbiología Ambiental, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Graduate Program in Chemistry, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Unidad Asociada de Microbiología del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Leandro D. Guerrero
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires, Argentina
| | - Leonardo Erijman
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ana Fernández-Scavino
- Laboratorio de Ecología Microbiana y Microbiología Ambiental, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
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Xu C, Shen S, Zhou B, Feng Y, He Z, Shi L, Wang Y, Wang H, Mishra T, Xue L. Long-term non-phosphorus application increased paddy methane emission by promoting organic acid and methanogen abundance in Tai Lake region, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161146. [PMID: 36566847 DOI: 10.1016/j.scitotenv.2022.161146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Rice paddy is a significant source of atmospheric methane (CH4), a major global warming source. CH4 emission from paddy fields is greatly influenced by phosphorus (P) management, especially the long-term non-P application on CH4 emission is largely unexplored. In the present study, long-term non-P application (NK) and P application (NPK) treatments of two paddy fields in Suzhou (from 1980) and Yixing (from 2009), Tai Lake region was done. The effect of P application on CH4 emissions and related microorganisms (i.e., methanogens and methanotrophs) from 2019 to 2020 was analyzed. Results revealed that long-term NK treatment didn't alter the seasonal trend of CH4 flux, but significantly promoted CH4 emissions at the tillering stage. The non-P application for >12 years caused the cumulative CH4 emissions of NK treatment in the whole rice season significantly increased by 41.9-221 % in two fields compared to NPK treatment in 2019 and 2020. NK treatment increased the abundance and diversity of methanogens, while reducing the abundance and diversity of methanotrophs. Community composition of soil pmoA gene differed in two experiment sites. Correlation analysis revealed that the CH4 emission was significant and positively related to soil mcrA gene and C/P while negatively related to soil pmoA gene and P. Structure equation model analysis show the low soil available P content was the dominant driving factor for the high CH4 emission under long-term non-P application through its direct impact on soil mcrA and pmoA genes. The increased soil organic acid content was another driver which was positively related to soil mcrA gene and negatively to soil pmoA gene. Our findings demonstrate the important role of soil P in regulating CH4 emissions from paddy fields in the Tai Lake region, China, and suitable P application is necessary for ensuring the yield while reducing CH4 emission.
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Affiliation(s)
- Chen Xu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212001, China
| | - Susu Shen
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Beibei Zhou
- College of Environment and Ecology, Jiangsu Open University, Nanjing 210017, China
| | - Yuanyuan Feng
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhu He
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Linlin Shi
- National Agricultural Experimental Station for Soil Quality, Suzhou Academy of Agricultural Sciences, Suzhou 215105, China
| | - Yu Wang
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Haihou Wang
- National Agricultural Experimental Station for Soil Quality, Suzhou Academy of Agricultural Sciences, Suzhou 215105, China
| | - Tripti Mishra
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lihong Xue
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212001, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Ma C, Wu J, Li F. Impacts of combined water-saving irrigation and controlled-release urea on CH 4 emission and its associated microbial communities and function. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154724. [PMID: 35331759 DOI: 10.1016/j.scitotenv.2022.154724] [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: 11/16/2021] [Revised: 03/02/2022] [Accepted: 03/17/2022] [Indexed: 06/08/2023]
Abstract
Water-saving irrigation and controlled-release nitrogen fertilizer are used in rice farming. The aim of this study was to understand the effects of water-saving irrigation and controlled-release urea on methane (CH4) emission and its associated microbial communities and function. A field experiment was conducted with two nitrogen treatments (NU 100% normal urea, CU 60% normal urea and 40% controlled-release urea, total N amount was the same) and three irrigation modes (CI continuous flooding irrigation, AI alternate wetting and drying irrigation, RI ridge irrigation). CH4 fluxes, organic acid contents and enzyme activities were measured, and soil microbial communities and function were investigated by whole-genome shotgun sequencing analysis, and then their relationships were analyzed by Spearman correlation analysis, redundancy analysis and mantel test. Compared to CI, AI and RI decreased cumulative CH4 emissions by 43.5% and 25.8% in NU, and 64.9% and 13.3% in CU, respectively. Among all treatments, AICU had the lowest CH4 emission and reduced it by 72.2% compared to CINU. AI and RI had higher contents of some organic acids than CI. Compared to CINU, AICU decreased the relative abundance of Methanosarcina barkeri and associated genes in the CO2-reduction methanogenesis pathway by 83.4% and 91.0%. Both abundance of methanogens and associated genes in the CO2-reduction methanogenesis pathway were positively correlated with cumulative CH4 emission, but negatively correlated with most soil organic acids. Thus AICU can mitigate CH4 emission by decreasing the abundance of methanogens and associated genes in the CO2-reduction methanogenesis pathway.
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Affiliation(s)
- Chenlei Ma
- College of Agriculture, Guangxi University, Nanning 530005, China
| | - Jiafa Wu
- College of Agriculture, Guangxi University, Nanning 530005, China; School of Marine Sciences and Biotechnology and Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning 530008, China
| | - Fusheng Li
- College of Agriculture, Guangxi University, Nanning 530005, China.
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Ammonia-oxidizing archaea in biological interactions. J Microbiol 2021; 59:298-310. [DOI: 10.1007/s12275-021-1005-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
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Liu X, Wang Y, Gu JD. Ecological distribution and potential roles of Woesearchaeota in anaerobic biogeochemical cycling unveiled by genomic analysis. Comput Struct Biotechnol J 2021; 19:794-800. [PMID: 33552450 PMCID: PMC7844129 DOI: 10.1016/j.csbj.2021.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/21/2022] Open
Abstract
Woesearchaeota as a newly established member of the superphylum DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) are surprisingly abundant and diverse in a wide variety of environments, including deep oil reservoir, sulfuric springs and anoxic aquifers, indicating a high diversity of their roles in global biogeochemical cycles. However, ecological functions of them remain elusive. To fill up this gap, we analyzed and compared the global distribution patterns of Woesearchaeota using the genomes available publicly. As a result, both ecological distribution patterns and metabolic predictions support a key role of woesearchaeotal lineages in cycling of carbon, nitrogen, and sulfur. Multivariate regression analysis reveals that Woesearchaeota might function in consortium with methanogens in the cycling of carbon in anaerobic environments, particularly in soils or sediments. Moreover, comparative genomic analysis and ecological distribution suggest the potential roles of Woesearchaeota in the processes of denitrification, nitrogen fixation, and dissimilatory nitrite reduction, especially in the wastewater treatment systems; and also uncovered the potential capability of sulfate reduction, sulfide oxidation and thiosulfate oxidation in sulfuric or sulfidic-rich environments. Our findings add more information into the ecological roles of archaea in the anoxic environment.
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Affiliation(s)
- Xiaobo Liu
- Environmental Engineering Program, Guangdong Technion-Israel Institute of Technology (GTIIT), 241 Daxue Road, Shantou 515063, Guangdong, China
| | - Yali Wang
- Conservation Center, Guangdong Museum, 2 Zhujiang East Road, Tianhe District, Guangzhou 510623, Guangdong, China
| | - Ji-Dong Gu
- Environmental Engineering Program, Guangdong Technion-Israel Institute of Technology (GTIIT), 241 Daxue Road, Shantou 515063, Guangdong, China
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Abstract
Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host-archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease.
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Jung J, Kim JS, Taffner J, Berg G, Ryu CM. Archaea, tiny helpers of land plants. Comput Struct Biotechnol J 2020; 18:2494-2500. [PMID: 33005311 PMCID: PMC7516179 DOI: 10.1016/j.csbj.2020.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/01/2020] [Accepted: 09/05/2020] [Indexed: 01/02/2023] Open
Abstract
Archaea are members of most microbiomes. While archaea are highly abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome. Only a few studies have investigated the role of archaea in plant health and its potential symbiosis in ecosystems. This review discusses recent progress in identifying how archaea contribute to plant traits such as growth, adaptation to abiotic stresses, and immune activation. We synthesized the most recent functional and molecular data on archaea, including root colonization and the volatile emission to activate plant systemic immunity. These data represent a paradigm shift in our understanding of plant-microbiota interactions.
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Affiliation(s)
- Jihye Jung
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, South Korea
- Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | - Jun-Seob Kim
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, South Korea
| | - Julian Taffner
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, South Korea
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Plant-archaea relationships: a potential means to improve crop production in arid and semi-arid regions. World J Microbiol Biotechnol 2020; 36:133. [PMID: 32772189 DOI: 10.1007/s11274-020-02910-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
Crop production in arid and semi-arid regions of the world is limited by several abiotic factors, including water stress, temperature extremes, low soil fertility, high soil pH, low soil water-holding capacity, and low soil organic matter. Moreover, arid and semi-arid areas experience low levels of rainfall with high spatial and temporal variability. Also, the indiscriminate use of chemicals, a practice that characterizes current agricultural practice, promotes crop and soil pollution potentially resulting in serious human health and environmental hazards. A reliable and sustainable alternative to current farming practice is, therefore, a necessity. One such option includes the use of plant growth-promoting microbes that can help to ameliorate some of the adverse effects of these multiple stresses. In this regard, archaea, functional components of the plant microbiome that are found both in the rhizosphere and the endosphere may contribute to the promotion of plant growth. Archaea can survive in extreme habitats such as areas with high temperatures and hypersaline water. No cases of archaea pathogenicity towards plants have been reported. Archaea appear to have the potential to promote plant growth, improve nutrient supply and protect plants against various abiotic stresses. A better understanding of recent developments in archaea functional diversity, plant colonizing ability, and modes of action could facilitate their eventual usage as reliable components of sustainable agricultural systems. The research discussed herein, therefore, addresses the potential role of archaea to improve sustainable crop production in arid and semi-arid areas.
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Ma Q, Li J, Aamer M, Huang G. Increasing methane (CH 4) emissions and altering rhizosphere microbial diversity in paddy soil by combining Chinese milk vetch and rice straw. PeerJ 2020; 8:e9653. [PMID: 32832274 PMCID: PMC7409806 DOI: 10.7717/peerj.9653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 07/13/2020] [Indexed: 11/20/2022] Open
Abstract
Background Chinese milk vetch (Astragalus sinicus L.) can improve paddy soil fertility and ecology through nitrogen fixation, but it can also increase greenhouse gas emissions. Our primary objective was to investigate how Chinese milk vetch, rice straw, and nitrogen fertilization affect the methane and microbial components of the rice rhizosphere. Methods We examined the rhizosphere's methane emissions and microbial abundance and diversity after incorporating Chinese milk vetch and rice straw into paddy soil. We used high-throughput sequencing of the 16s rRNA and ITS1 genes to study changes in the bacterial and fungal communities, respectively. Over the course of our experiment, we applied seven different treatments to the paddy soil: conventional fertilization (the control treatment) for winter fallow crops, three levels of nitrogen in Chinese milk vetch, and three levels of nitrogen in Chinese milk vetch combined with rice straw. Results Rice yield and methane emissions increased during cultivation when the soil was treated with Chinese milk vetch with and without added straw. The nitrogen application also affected the methane fluxes. Alpha diversity measurements showed that Chinese milk vetch increased the diversity of the soil fungal community but did not significantly affect the bacterial community. Chinese milk vetch affected the rhizosphere microorganism communities by increasing the number of Methanomicrobia.
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Affiliation(s)
- Qiaoying Ma
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jiwei Li
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Muhammad Aamer
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Guoqin Huang
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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Novel insights into plant-associated archaea and their functioning in arugula ( Eruca sativa Mill.). J Adv Res 2019; 19:39-48. [PMID: 31341668 PMCID: PMC6629838 DOI: 10.1016/j.jare.2019.04.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 01/21/2023] Open
Abstract
A plant's microbiota has various implications for the plant's health and performance; however, the roles of many microbial lineages, particularly Archaea, have not been explored in detail. In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of a common salad plant, arugula (Eruca sativa Mill.). The archaeal communities associated with the soil, rhizosphere and phyllosphere were distinct, but a high proportion of community members were shared among all analysed habitats. Soil habitats exhibited the highest diversity of Archaea, followed by the rhizosphere and the phyllosphere. The archaeal community was dominated by Thaumarchaeota and Euryarchaeota, with the most abundant taxa assigned to Candidatus Nitrosocosmicus, species of the 'Soil Crenarchaeotic Group' and, interestingly, Methanosarcina. Moreover, a large number of archaea-assigned sequences remained unassigned at lower taxonomic levels. Overall, analysis of shotgun-sequenced total-community DNA revealed a more diverse archaeome. Differences were evident at the class level and at higher taxonomic resolutions when compared to results from the 16S rRNA gene fragment amplicon library. Functional assessments primarily revealed archaeal genes related to response to stress (especially oxidative stress), CO2 fixation, and glycogen degradation. Microscopic visualizations of fluorescently labelled archaea in the phyllosphere revealed small scattered colonies, while archaea in the rhizosphere were found to be embedded within large bacterial biofilms. Altogether, Archaea were identified as a rather small but niche-specific component of the microbiomes of the widespread leafy green plant arugula.
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Three-Source Partitioning of Methane Emissions from Paddy Soil: Linkage to Methanogenic Community Structure. Int J Mol Sci 2019; 20:ijms20071586. [PMID: 30934889 PMCID: PMC6479939 DOI: 10.3390/ijms20071586] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 11/17/2022] Open
Abstract
Identification of the carbon (C) sources of methane (CH4) and methanogenic community structures after organic fertilization may provide a better understanding of the mechanism that regulate CH4 emissions from paddy soils. Based on our previous field study, a pot experiment with isotopic 13C labelling was designed in this study. The objective was to investigate the main C sources for CH4 emissions and the key environmental factor with the application of organic fertilizer in paddies. Results indicated that 28.6%, 64.5%, 0.4%, and 6.5% of 13C was respectively distributed in CO2, the plants, soil, and CH4 at the rice tillering stage. In total, organically fertilized paddy soil emitted 3.51 kg·CH4 ha−1 vs. 2.00 kg·CH4 ha−1 for the no fertilizer treatment. Maximum CH4 fluxes from organically fertilized (0.46 mg·m−2·h−1) and non-fertilized (0.16 mg·m−2·h−1) soils occurred on day 30 (tillering stage). The total percentage of CH4 emissions derived from rice photosynthesis C was 49%, organic fertilizer C < 0.34%, and native soil C > 51%. Therefore, the increased CH4 emissions from paddy soil after organic fertilization were mainly derived from native soil and photosynthesis. The 16S rRNA sequencing showed Methanosarcina (64%) was the dominant methanogen in paddy soil. Organic fertilization increased the relative abundance of Methanosarcina, especially in rhizosphere. Additionally, Methanosarcina sp. 795 and Methanosarcina sp. 1H1 co-occurred with Methanobrevibacter sp. AbM23, Methanoculleus sp. 25XMc2, Methanosaeta sp. HA, and Methanobacterium sp. MB1. The increased CH4 fluxes and labile methanogenic community structure in organically fertilized rice soil were primarily due to the increased soil C, nitrogen, potassium, phosphate, and acetate. These results highlight the contributions of native soil- and photosynthesis-derived C in paddy soil CH4 emissions, and provide basis for more complex investigations of the pathways involved in ecosystem CH4 processes.
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Archaea: forgotten players in the microbiome. Emerg Top Life Sci 2018; 2:459-468. [PMID: 33525830 DOI: 10.1042/etls20180035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 10/01/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022]
Abstract
Archaea, the third domain of life containing unique membrane composition and highly diverse cell wall structures, were only recognized 40 years ago. Initially identified in extreme environments, they are currently recognized as organisms ubiquitously present in most, if not all, microbiomes associated with eukaryotic hosts. However, they have been mostly overseen in microbiome studies due to the lack of standardized detection protocols and to the fact that no archaeal pathogen is currently known. Recent years clearly showed that (i) archaea are part of the microbiomes associated with plants, animals and humans, (ii) form biofilms and (iii) interact and activate the human immune system. Future studies will not only define the host-associated diversity of archaea (referred to as 'archaeome') but also contribute to our understanding of the comprehensive metabolic interplay between archaea and bacteria and the long-term gain insights into their role in human health and their potential role(s) during disease development.
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Yuan J, Yuan Y, Zhu Y, Cao L. Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:770-781. [PMID: 29426201 DOI: 10.1016/j.scitotenv.2018.01.233] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Paddy soil accounts for 10% of global atmospheric methane (CH4) emissions. Many types of fertilizers may enhance CH4 emissions, especially organic fertilizer. The aim of this study was to explore the effects of different fertilizers on CH4 and methanogen patterns in paddy soil. This experiment involved four treatments: chemical fertilizer (CT), organic fertilizer (OT), mixed with chemical and organic fertilizer (MT), and no fertilizer (ctrl). The three fertilization treatments were applied with total nitrogen at the same rate of 300 kg N ha-1. Paddy CH4, soil physicochemical variables and methanogen communities were quantitatively analyzed. Rhizosphere soil mcrA and pmoA gene copy numbers were determined by qPCR. Methanogenic 16S rRNA genes were identified by MiSeq sequencing. The results indicated CH4 emissions were significantly higher in OT (145.31 kg ha-1) than MT (84.62 kg ha-1), CT (77.88 kg ha-1) or ctrl (32.19 kg ha-1). Soil organic acids were also increased by organic fertilization. CH4 effluxes were significantly and negatively related to mcrA and pmoA gene copy numbers, and positively related to mcrA/pmoA. Above all, hydrogenotrophic Methanocella and acetoclastic Methanosaeta were the predominant methanogenic communities; these communities were strictly associated with soil potassium, oxalate, acetate, and succinate. Application of organic fertilizer promoted the dominant acetoclastic methanogens, but suppressed the dominant hydrogenotrophic methanogens. The transformation in methanogenic community structure and enhanced availability of C substrates may explain the increased CH4 production in OT compared to other treatments. Compared to OT, MT may partially mitigate CH4 emissions while guaranteeing a high rice yield. On this basis, we recommend the local fertilization pattern should change from 300 N kg ha-1 of organic manure to the same level of mixed fertilization. Moreover, we suggest multiple combinations of mixed fertilization merit more investigation in the future.
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Affiliation(s)
- Jing Yuan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yongkun Yuan
- Irrigation Technology Extension Station of Qingpu, 2 Yuan Road, Shanghai 201707, China
| | - Yihang Zhu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Linkui Cao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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16
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What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs. mSphere 2018; 3:3/3/e00122-18. [PMID: 29743201 PMCID: PMC5956146 DOI: 10.1128/msphere.00122-18] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/15/2018] [Indexed: 11/20/2022] Open
Abstract
Archaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress. The Archaea represent a significant component of the plant microbiome, whereas their function is still unclear. Different plant species representing the natural vegetation of alpine bogs harbor a substantial archaeal community originating from five phyla, 60 genera, and 334 operational taxonomic units (OTUs). We identified a core archaeome for all bog plants and ecosystem-specific, so far unclassified Archaea. In the metagenomic data set, Archaea were found to have the potential to interact with plants by (i) possible plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic (especially oxidative and osmotic) stress. The unexpectedly high degree of plant specificity supports plant-archaeon interactions. Moreover, functional signatures of Archaea reveal genetic capacity for the interplay with fungi and an important role in the carbon and nitrogen cycle: e.g., CO2 and N2 fixation. These facts reveal an important, yet unobserved role of the Archaea for plants as well as for the bog ecosystem. IMPORTANCEArchaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress.
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17
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In 't Zandt MH, Beckmann S, Rijkers R, Jetten MSM, Manefield M, Welte CU. Nutrient and acetate amendment leads to acetoclastic methane production and microbial community change in a non-producing Australian coal well. Microb Biotechnol 2017; 11:626-638. [PMID: 28925579 PMCID: PMC6011947 DOI: 10.1111/1751-7915.12853] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 11/29/2022] Open
Abstract
Coal mining is responsible for 11% of total anthropogenic methane emission thereby contributing considerably to climate change. Attempts to harvest coalbed methane for energy production are challenged by relatively low methane concentrations. In this study, we investigated whether nutrient and acetate amendment of a non-producing sub-bituminous coal well could transform the system to a methane source. We tracked cell counts, methane production, acetate concentration and geochemical parameters for 25 months in one amended and one unamended coal well in Australia. Additionally, the microbial community was analysed with 16S rRNA gene amplicon sequencing at 17 and 25 months after amendment and complemented by metagenome sequencing at 25 months. We found that cell numbers increased rapidly from 3.0 × 104 cells ml-1 to 9.9 × 107 in the first 7 months after amendment. However, acetate depletion with concomitant methane production started only after 12-19 months. The microbial community was dominated by complex organic compound degraders (Anaerolineaceae, Rhodocyclaceae and Geobacter spp.), acetoclastic methanogens (Methanothrix spp.) and fungi (Agaricomycetes). Even though the microbial community had the functional potential to convert coal to methane, we observed no indication that coal was actually converted within the time frame of the study. Our results suggest that even though nutrient and acetate amendment stimulated relevant microbial species, it is not a sustainable way to transform non-producing coal wells into bioenergy factories.
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Affiliation(s)
- Michiel H In 't Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Netherlands Earth Systems Science Center, Utrecht University, Heidelberglaan 2, 3584 CS, Utrecht, The Netherlands
| | - Sabrina Beckmann
- School of Chemical Engineering, School of Civil and Environmental Engineering, University of New South Wales, High Street, 2052, Sydney, NSW, Australia
| | - Ruud Rijkers
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Netherlands Earth Systems Science Center, Utrecht University, Heidelberglaan 2, 3584 CS, Utrecht, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike Manefield
- School of Chemical Engineering, School of Civil and Environmental Engineering, University of New South Wales, High Street, 2052, Sydney, NSW, Australia
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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18
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Moissl-Eichinger C, Pausan M, Taffner J, Berg G, Bang C, Schmitz RA. Archaea Are Interactive Components of Complex Microbiomes. Trends Microbiol 2017; 26:70-85. [PMID: 28826642 DOI: 10.1016/j.tim.2017.07.004] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/06/2017] [Accepted: 07/21/2017] [Indexed: 02/06/2023]
Abstract
Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed 'primitiveness'. The archaea constitute a considerable fraction of the Earth's ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes - in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain.
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Affiliation(s)
| | - Manuela Pausan
- Medical University Graz, Internal Medicine, Graz, Austria
| | | | | | - Corinna Bang
- Christian-Albrechts-University Kiel, Kiel, Germany
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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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20
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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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