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Wang S, Sun P, Liu J, Xu Y, Dolfing J, Wu Y. Distribution of methanogenic and methanotrophic consortia at soil-water interfaces in rice paddies across climate zones. iScience 2022; 26:105851. [PMID: 36636345 PMCID: PMC9829807 DOI: 10.1016/j.isci.2022.105851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Periphytic biofilms (PB) at the soil-water interface contributes 7-38% of the methane emission from rice paddies, yet the biogeographical mechanism underlying and affecting the process remain elusive. In this study, rice fields along an edapho-vclimatic gradient were sampled, and the environmental drivers affecting distribution of methanogenic and methanotrophic communities were evaluated. The methanogenic and methanotrophic communities at soil-water interface showed less complex inter/intra-generic interactions than those in soil, and their relative abundances were weakly driven by spatial distance, soil organic carbon, soil total nitrogen and pH. The nutrient supply and buffering capacity of extracellular polymeric substance released by PB reduced their interaction and enhanced the resilience on edaphic environment changes. Climate affected soil metal content, extracellular polymeric substance content, and thus the methane-related communities, and caused geographical variation in the impacts of PB on methane emissions from rice paddies. This study facilitates our understanding of geographical differences in the contribution of PB to methane emission.
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Affiliation(s)
- Sichu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Institute of Agricultural Resources and Environment, Jiangsu Academy of Agriculture Sciences (JAAS), 50 Zhongling Road, Nanjing 210014, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Pengfei Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Junzhuo Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Ying Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle upon Tyne NE1 8QH, UK
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People’s Republic of China, Shuitianba Zigui, Yichang 443605, China,Corresponding author
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Takeuchi M, Yoshioka H. Acetate excretion by a methanotroph, Methylocaldum marinum S8, under aerobic conditions. Biosci Biotechnol Biochem 2021; 85:2326-2333. [PMID: 34459486 DOI: 10.1093/bbb/zbab150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/25/2021] [Indexed: 11/14/2022]
Abstract
Methane-oxidizing bacteria (methanotrophs) often coexist with methylotrophs that utilize methanol excreted by methanotrophs. Recently, we found that a facultative methylotroph, Methyloceanibacter caenitepidi Gela4T, possibly utilizes acetate rather than methanol in the coculture with a methanotroph, Methylocaldum marinum S8. Here, we examined the effects of oxygen concentrations on growth of and acetate excretion by M. marinum S8 in pure culture and the coculture with M. caenitepidi Gela4T. M. marinum S8 excreted acetate during the exponential growth phase not only under microaerobic (O2 concentrations of 3.5%-6%) but also under aerobic (O2 concentrations of 20%-31%) conditions. RNA-Seq analyses of M. marinum S8 cells grown under aerobic conditions suggested that phosphoketolase and acetate kinase were candidate genes involved in acetate production. Nonmethylotrophic bacteria, Cupriavidus necator NBRC 102504, could grow when cocultured with M. marinum S8, also supporting the existence of methanol-independent cross-feeding from M. marinum S8 under aerobic conditions.
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Affiliation(s)
- Mio Takeuchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Midorigaoka, Ikeda, Osaka, Japan
| | - Hideyoshi Yoshioka
- Institute for Geo-resources and Environments, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki, Japan
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Methane utilizing plant growth-promoting microbial diversity analysis of flooded paddy ecosystem of India. World J Microbiol Biotechnol 2021; 37:56. [PMID: 33619649 DOI: 10.1007/s11274-021-03018-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2021] [Indexed: 01/10/2023]
Abstract
Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH4) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH4 utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, Ks of 1.92 ± 0.092 mg CH4 L-1. Besides the ability to utilize CH4, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.
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Zhang Q, Yang G, Song Y, Kou D, Wang G, Zhang D, Qin S, Mao C, Feng X, Yang Y. Magnitude and Drivers of Potential Methane Oxidation and Production across the Tibetan Alpine Permafrost Region. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14243-14252. [PMID: 31718180 DOI: 10.1021/acs.est.9b03490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Methane (CH4) dynamics across permafrost regions is critical in determining the magnitude and direction of permafrost carbon (C)-climate feedback. However, current studies are mainly derived from the Arctic area, with limited evidence from other permafrost regions. By combining large-scale laboratory incubation across 51 sampling sites with machine learning techniques and bootstrap analysis, here, we determined regional patterns and dominant drivers of CH4 oxidation potential in alpine steppe and meadow (CH4 sink areas) and CH4 production potential in swamp meadow (CH4 source areas) across the Tibetan alpine permafrost region. Our results showed that both CH4 oxidation potential (in alpine steppe and meadow) and CH4 production potential (in swamp meadow) exhibited large variability across various sampling sites, with the median value being 8.7, 9.6, and 11.5 ng g-1 dry soil h-1, respectively. Our results also revealed that methanotroph abundance and soil moisture were two dominant factors regulating CH4 oxidation potential, whereas CH4 production potential was mainly affected by methanogen abundance and the soil organic carbon content, with functional gene abundance acting as the best explaining variable. These results highlight the crucial role of microbes in regulating CH4 dynamics, which should be considered when predicting the permafrost C cycle under future climate scenarios.
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Affiliation(s)
- Qiwen Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany , Chinese Academy of Sciences , Beijing 100093 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Guibiao Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany , Chinese Academy of Sciences , Beijing 100093 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yutong Song
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany , Chinese Academy of Sciences , Beijing 100093 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Dan Kou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany , Chinese Academy of Sciences , Beijing 100093 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Guanqin Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany , Chinese Academy of Sciences , Beijing 100093 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Dianye Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany , Chinese Academy of Sciences , Beijing 100093 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany , Chinese Academy of Sciences , Beijing 100093 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Chao Mao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany , Chinese Academy of Sciences , Beijing 100093 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xuehui Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany , Chinese Academy of Sciences , Beijing 100093 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany , Chinese Academy of Sciences , Beijing 100093 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
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Yarwood SA. The role of wetland microorganisms in plant-litter decomposition and soil organic matter formation: a critical review. FEMS Microbiol Ecol 2019; 94:5087730. [PMID: 30169564 DOI: 10.1093/femsec/fiy175] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 08/29/2018] [Indexed: 02/06/2023] Open
Abstract
New soil organic matter (SOM) models highlight the role of microorganisms in plant litter decomposition and storage of microbial-derived carbon (C) molecules. Wetlands store more C per unit area than any other ecosystem, but SOM storage mechanisms such as aggregation and metal complexes are mostly untested in wetlands. This review discusses what is currently known about the role of microorganisms in SOM formation and C sequestrations, as well as, measures of microbial communities as they relate to wetland C cycling. Studies within the last decade have yielded new insights about microbial communities. For example, microbial communities appear to be adapted to short-term fluctuations in saturation and redox and researchers have observed synergistic pairings that in some cases run counter to thermodynamic theory. Significant knowledge gaps yet to be filled include: (i) What controls microbial access to and decomposition of plant litter and SOM? (ii) How does microbial community structure shape C fate, across different wetland types? (iii) What types of plant and microbial molecules contribute to SOM accumulation? Studies examining the active microbial community directly or that utilize multi-pronged approaches are shedding new light on microbial functional potential, however, and promise to improve wetland C models in the near future.
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Affiliation(s)
- Stephanie A Yarwood
- Environmental Science and Technology Department, University of Maryland, 1204 HJ Patterson Hall, College Park, MD 20742, USA
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6
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Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8. PLoS One 2019; 14:e0213535. [PMID: 30870453 PMCID: PMC6417678 DOI: 10.1371/journal.pone.0213535] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/22/2019] [Indexed: 11/19/2022] Open
Abstract
Non-methanotrophic bacteria such as methylotrophs often coexist with methane-oxidizing bacteria (methanotrophs) by cross-feeding on methane-derived carbon. Methanol has long been considered a major compound that mediates cross-feeding of methane-derived carbon. Despite the potential importance of cross-feeding in the global carbon cycle, only a few studies have actually explored metabolic responses of a bacteria when cross-feeding on a methanotroph. Recently, we isolated a novel facultative methylotroph, Methyloceanibacter caenitepidi Gela4, which grows syntrophically with the methanotroph, Methylocaldum marinum S8. To assess the potential metabolic pathways in M. caenitepidi Gela4 co-cultured with M. marinum S8, we conducted genomic analyses of the two strains, as well as RNA-Seq and chemical analyses of M. caenitepidi Gela4, both in pure culture with methanol and in co-culture with methanotrophs. Genes involved in the serine pathway were downregulated in M. caenitepidi Gela4 under co-culture conditions, and methanol was below the detection limit (< 310 nM) in both pure culture of M. marinum S8 and co-culture. In contrast, genes involved in the tricarboxylic acid cycle, as well as acetyl-CoA synthetase, were upregulated in M. caenitepidi Gela4 under co-culture conditions. Notably, a pure culture of M. marinum S8 produced acetate (< 16 μM) during growth. These results suggested that an organic compound other than methanol, possibly acetate, might be the major carbon source for M. caenitepidi Gela4 cross-fed by M. marinum S8. Co-culture of M. caenitepidi Gela4 and M. marinum S8 may represent a model system to further study methanol-independent cross-feeding from methanotrophs to non-methanotrophic bacteria.
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7
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Jiang B, Jin N, Xing Y, Su Y, Zhang D. Unraveling uncultivable pesticide degraders via stable isotope probing (SIP). Crit Rev Biotechnol 2018; 38:1025-1048. [DOI: 10.1080/07388551.2018.1427697] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Naifu Jin
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Yuping Su
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
- School of Environment, Tsinghua University, Beijing, PR China
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Kwon MJ, Beulig F, Ilie I, Wildner M, Küsel K, Merbold L, Mahecha MD, Zimov N, Zimov SA, Heimann M, Schuur EAG, Kostka JE, Kolle O, Hilke I, Göckede M. Plants, microorganisms, and soil temperatures contribute to a decrease in methane fluxes on a drained Arctic floodplain. GLOBAL CHANGE BIOLOGY 2017; 23:2396-2412. [PMID: 27901306 DOI: 10.1111/gcb.13558] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 05/06/2023]
Abstract
As surface temperatures are expected to rise in the future, ice-rich permafrost may thaw, altering soil topography and hydrology and creating a mosaic of wet and dry soil surfaces in the Arctic. Arctic wetlands are large sources of CH4 , and investigating effects of soil hydrology on CH4 fluxes is of great importance for predicting ecosystem feedback in response to climate change. In this study, we investigate how a decade-long drying manipulation on an Arctic floodplain influences CH4 -associated microorganisms, soil thermal regimes, and plant communities. Moreover, we examine how these drainage-induced changes may then modify CH4 fluxes in the growing and nongrowing seasons. This study shows that drainage substantially lowered the abundance of methanogens along with methanotrophic bacteria, which may have reduced CH4 cycling. Soil temperatures of the drained areas were lower in deep, anoxic soil layers (below 30 cm), but higher in oxic topsoil layers (0-15 cm) compared to the control wet areas. This pattern of soil temperatures may have reduced the rates of methanogenesis while elevating those of CH4 oxidation, thereby decreasing net CH4 fluxes. The abundance of Eriophorum angustifolium, an aerenchymatous plant species, diminished significantly in the drained areas. Due to this decrease, a higher fraction of CH4 was alternatively emitted to the atmosphere by diffusion, possibly increasing the potential for CH4 oxidation and leading to a decrease in net CH4 fluxes compared to a control site. Drainage lowered CH4 fluxes by a factor of 20 during the growing season, with postdrainage changes in microbial communities, soil temperatures, and plant communities also contributing to this reduction. In contrast, we observed CH4 emissions increased by 10% in the drained areas during the nongrowing season, although this difference was insignificant given the small magnitudes of fluxes. This study showed that long-term drainage considerably reduced CH4 fluxes through modified ecosystem properties.
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Affiliation(s)
- Min Jung Kwon
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
| | - Felix Beulig
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburgerstr 159, 07743 Jena, Germany
| | - Iulia Ilie
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
| | - Marcus Wildner
- Geoecology-Environmental Science: Micrometeorology and Atmospheric Chemistry, Faculty of Biology, Chemistry and Earth Science, University of Bayreuth, Universitätsstr 30, 95447 Bayreuth, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburgerstr 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5d, 04103, Leipzig, Germany
| | - Lutz Merbold
- Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, Universitätstr 16, 8092 Zürich, Switzerland
| | - Miguel D Mahecha
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5d, 04103, Leipzig, Germany
| | - Nikita Zimov
- North-East Science Station, Pacific Institute for Geography, Far-Eastern Branch of Russian Academy of Science, PO Box 18, Cherskii, Republic of Sakha (Yakutia), Russia
| | - Sergey A Zimov
- North-East Science Station, Pacific Institute for Geography, Far-Eastern Branch of Russian Academy of Science, PO Box 18, Cherskii, Republic of Sakha (Yakutia), Russia
| | - Martin Heimann
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
- Division of Atmospheric Sciences, Department of Physics, PO Box 64, FI-00014 University of Helsinki, Helsinki, Finland
| | - Edward A G Schuur
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, PO Box 5620, Flagstaff, AZ 86011, USA
| | - Joel E Kostka
- School of Biology, Georgia Institute of Technology, North Avenue, Atlanta, GA 30332, USA
| | - Olaf Kolle
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
| | - Ines Hilke
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
| | - Mathias Göckede
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str 10, 07745 Jena, Germany
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Reche MHLR, Reali C, Pittol M, de Athayde Saul D, Macedo VRM, Valiati VH, Machado V, Fiuza LM. Diversity of culturable Gram-negative bacteria isolated from irrigation water of two rice crop regions in Southern Brazil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:359. [PMID: 27197729 DOI: 10.1007/s10661-016-5357-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 05/09/2016] [Indexed: 06/05/2023]
Abstract
In this study, we assessed the diversity of Gram-negative bacteria found in water used for irrigation of rice crops in two growing areas of southern Brazil. Samples were collected from the main irrigation channel and field drain area. Twenty-two bacterial species were found in Cachoeirinha and 28 in Camaquã. In both areas, the most frequent bacterial families were Enterobacteriaceae and Aeromonadaceae. Differences in microbial diversity were observed in both study areas. Thirty-five Gram-negative species were identified; however, only 15 were common in both locations. In addition, there were found pathogenic and drug-resistant species, such as Acinetobacter sp., Brucella spp., and Chryseobacterium meningosepticum. This study demonstrates the existence of a number of pathogenic species in aquatic ecosystems analyzed in three consecutive crop years, especially water used for rice production.
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Affiliation(s)
- Maria Helena Lima Ribeiro Reche
- Microbiology and Toxicology Laboratory, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
- Postgraduate Program in Biology, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
| | - Catiusca Reali
- Microbiology and Toxicology Laboratory, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
- Postgraduate Program in Biology, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
| | - Michele Pittol
- Microbiology and Toxicology Laboratory, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
- Postgraduate Program in Biology, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
| | - Danilo de Athayde Saul
- Microbiology and Toxicology Laboratory, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
- Postgraduate Program in Biology, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
| | - Vera Regina Mussoi Macedo
- Microbiology and Toxicology Laboratory, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
- Postgraduate Program in Biology, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
- Molecular Biology Laboratory, PPG, Universidade do Vale do Rio dos Sinos (UNISINOS), Av. Unisinos, 950 - Bairro Cristo Rei - CEP, 93.022-750, São Leopoldo, Brazil
| | - Victor Hugo Valiati
- Postgraduate Program in Biology, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil.
- Molecular Biology Laboratory, PPG, Universidade do Vale do Rio dos Sinos (UNISINOS), Av. Unisinos, 950 - Bairro Cristo Rei - CEP, 93.022-750, São Leopoldo, Brazil.
| | - Vilmar Machado
- Microbiology and Toxicology Laboratory, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
- Postgraduate Program in Biology, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
- Molecular Biology Laboratory, PPG, Universidade do Vale do Rio dos Sinos (UNISINOS), Av. Unisinos, 950 - Bairro Cristo Rei - CEP, 93.022-750, São Leopoldo, Brazil
| | - Lidia Mariana Fiuza
- Microbiology and Toxicology Laboratory, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
- Postgraduate Program in Biology, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
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10
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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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11
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Yoshida N, Iguchi H, Yurimoto H, Murakami A, Sakai Y. Aquatic plant surface as a niche for methanotrophs. Front Microbiol 2014; 5:30. [PMID: 24550901 PMCID: PMC3909826 DOI: 10.3389/fmicb.2014.00030] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/17/2014] [Indexed: 11/13/2022] Open
Abstract
This study investigated the potential local CH4 sink in various plant parts as a boundary environment of CH4 emission and consumption. By comparing CH4 consumption activities in cultures inoculated with parts from 39 plant species, we observed significantly higher consumption of CH4 associated with aquatic plants than other emergent plant parts such as woody plant leaves, macrophytic marine algae, and sea grass. In situ activity of CH4 consumption by methanotrophs associated with different species of aquatic plants was in the range of 3.7–37 μmol·h−1·g−1 dry weight, which was ca 5.7–370-fold higher than epiphytic CH4 consumption in submerged parts of emergent plants. The qPCR-estimated copy numbers of the particulate methane monooxygenase-encoding gene pmoA were variable among the aquatic plants and ranged in the order of 105–107 copies·g−1 dry weight, which correlated with the observed CH4 consumption activities. Phylogenetic identification of methanotrophs on aquatic plants based on the pmoA sequence analysis revealed a predominance of diverse gammaproteobacterial type-I methanotrophs, including a phylotype of a possible plant-associated methanotroph with the closest identity (86–89%) to Methylocaldum gracile.
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Affiliation(s)
- Naoko Yoshida
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University Kyoto, Japan ; Center for Fostering Young and Innovative Researchers, Nagoya Institute of Technology, Nagoya Aichi, Japan
| | - Hiroyuki Iguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University Kyoto, Japan
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University Kyoto, Japan
| | - Akio Murakami
- Kobe University Research Center for Inland Seas Awaji, Hyogo, Japan ; Japan Science and Technology Agency, CREST Awaji, Hyogo, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University Kyoto, Japan ; Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency Tokyo, Japan
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12
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Ikeda S, Sasaki K, Okubo T, Yamashita A, Terasawa K, Bao Z, Liu D, Watanabe T, Murase J, Asakawa S, Eda S, Mitsui H, Sato T, Minamisawa K. Low nitrogen fertilization adapts rice root microbiome to low nutrient environment by changing biogeochemical functions. Microbes Environ 2014; 29:50-9. [PMID: 24463575 PMCID: PMC4041235 DOI: 10.1264/jsme2.me13110] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reduced fertilizer usage is one of the objectives of field management in the pursuit of sustainable agriculture. Here, we report on shifts of bacterial communities in paddy rice ecosystems with low (LN), standard (SN), and high (HN) levels of N fertilizer application (0, 30, and 300 kg N ha−1, respectively). The LN field had received no N fertilizer for 5 years prior to the experiment. The LN and HN plants showed a 50% decrease and a 60% increase in biomass compared with the SN plant biomass, respectively. Analyses of 16S rRNA genes suggested shifts of bacterial communities between the LN and SN root microbiomes, which were statistically confirmed by metagenome analyses. The relative abundances of Burkholderia, Bradyrhizobium and Methylosinus were significantly increased in root microbiome of the LN field relative to the SN field. Conversely, the abundance of methanogenic archaea was reduced in the LN field relative to the SN field. The functional genes for methane oxidation (pmo and mmo) and plant association (acdS and iaaMH) were significantly abundant in the LN root microbiome. Quantitative PCR of pmoA/mcrA genes and a 13C methane experiment provided evidence of more active methane oxidation in the rice roots of the LN field. In addition, functional genes for the metabolism of N, S, Fe, and aromatic compounds were more abundant in the LN root microbiome. These results suggest that low-N-fertilizer management is an important factor in shaping the microbial community structure containing key microbes for plant associations and biogeochemical processes in paddy rice ecosystems.
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Affiliation(s)
- Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University
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13
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Thong-On A, Suzuki K, Noda S, Inoue JI, Kajiwara S, Ohkuma M. Isolation and characterization of anaerobic bacteria for symbiotic recycling of uric acid nitrogen in the gut of various termites. Microbes Environ 2012; 27:186-92. [PMID: 22791052 PMCID: PMC4036019 DOI: 10.1264/jsme2.me11325] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recycling of the nitrogenous waste uric acid (UA) of wood-feeding termites by their gut bacteria is one of the significant aspects of symbiosis for the conservation of nitrogen sources. Diverse anaerobic UA-degrading bacteria comprising 16 species were isolated from the gut of eight termite species, and were assigned to Clostridia, Enterobacteriaceae, and low G+C Gram-positive cocci. UA-degrading Clostridia had never been isolated from termite guts. UA-degrading ability was sporadically distributed among phylogenetically various culturable anaerobic bacteria from termite guts. A strain of Clostridium sp., which was commonly isolated from three termite species and represented a probable new species in cluster XIVa of clostridia, utilized UA as a nitrogen source but not as a sole carbon and energy source. This feature is in clear contrast to that of well-studied purinolytic clostridia or previously isolated UA degraders from termite guts, which also utilize UA as a sole carbon and energy source. Ammonia is the major nitrogenous product of UA degradation. Various purines stimulated the growth of this strain when added to an otherwise growth-limiting, nitrogen poor medium. The bacterial species involved the recycling of UA nitrogen in the gut microbial community of termites are more diverse in terms of both taxonomy and nutritional physiology than previously recognized.
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Affiliation(s)
- Arunee Thong-On
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
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14
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Okubo T, Ikeda S, Yamashita A, Terasawa K, Minamisawa K. Pyrosequence read length of 16S rRNA gene affects phylogenetic assignment of plant-associated bacteria. Microbes Environ 2012; 27:204-8. [PMID: 22791055 PMCID: PMC4036018 DOI: 10.1264/jsme2.me11258] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pyrosequence targeting of the 16S rRNA gene has been adopted for microbial communities associated with field-grown plants. To examine phylogenetic drifts according to read length and bioinformatic tools, original and chopped sequences (250–570 bp) covering the V1–V4 regions of 16S rRNA genes were compared using pyrosequence and Sanger reads of rice root microbiomes. The phylogenetic assignment at genus level depended on read length, especially in the genus Bradyrhizobium, which is one of the ecologically important bacterial genera associated with plants. We discuss the methodology of phylogenetic assignments of plant-associated bacteria by 16S rRNA pyrosequence.
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Affiliation(s)
- Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
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15
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Singh JS, Singh DP. Reforestation: A potential approach to mitigate excess atmospheric CH4build-up. ECOLOGICAL MANAGEMENT & RESTORATION 2012. [DOI: 10.1111/emr.12004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Dianou D, Ueno C, Ogiso T, Kimura M, Asakawa S. Diversity of cultivable methane-oxidizing bacteria in microsites of a rice paddy field: investigation by cultivation method and fluorescence in situ hybridization (FISH). Microbes Environ 2012; 27:278-87. [PMID: 22446309 PMCID: PMC4036049 DOI: 10.1264/jsme2.me11327] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The diversity of cultivable methane-oxidizing bacteria (MOB) in the rice paddy field ecosystem was investigated by combined culture-dependent and fluorescence in situ hybridization (FISH) techniques. Seven microsites of a Japanese rice paddy field were the focus of the study: floodwater, surface soil, bulk soil, rhizosphere soil, root, basal stem of rice plant, and rice stumps of previous harvest. Based on pmoA gene analysis and transmission electron microscopy (TEM), four type I, and nine type II MOB isolates were obtained from the highest dilution series of enrichment cultures. The type I MOB isolates included a novel species in the genus Methylomonas from floodwater and this is the first type I MOB strain isolated from floodwater of a rice paddy field. In the type I MOB, two isolates from stumps were closely related to Methylomonas spp.; one isolate obtained from rhizosphere soil was most related to Methyloccocus-Methylocaldum-Methylogaea clade. Almost all the type II MOB isolates were related to Methylocystis methanotrophs. FISH confirmed the presence of both types I and II MOB in all the microsites and in the related enrichment cultures. The study reported, for the first time, the diversity of cultivable methanotrophs including a novel species of type I MOB in rice paddy field compartments. Refining growth media and culture conditions, in combination with molecular approaches, will allow us to broaden our knowledge on the MOB community in the rice paddy field ecosystem and consequently to implement strategies for mitigating CH4 emission from this ecosystem.
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Affiliation(s)
- Dayéri Dianou
- Centre National de la Recherche Scientifique et Technologique, 03BP7192 Ouagadougou, Burkina Faso
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17
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Ishii S, Ikeda S, Minamisawa K, Senoo K. Nitrogen cycling in rice paddy environments: past achievements and future challenges. Microbes Environ 2011; 26:282-92. [PMID: 22008507 DOI: 10.1264/jsme2.me11293] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nitrogen is generally the most limiting nutrient for rice production. In rice paddy soils, various biochemical processes can occur regarding N cycling, including nitrification, denitrification, and nitrogen fixation. Since its discovery in the 1930s, the nitrification-denitrification process has been extensively studied in Japan. It may cause N loss from rice paddy soils, while it can also reduce environmental pollutions such as nitrate leaching and emission of nitrous oxide (N(2)O). In this review article, we first summarize the early and important findings regarding nitrification-denitrification in rice paddy soils, and then update recent findings regarding key players in denitrification and N(2)O reduction. In addition, we also discuss the potential occurrence of other newly found reactions in the N cycle, such as archaeal ammonia oxidization, fungal denitrification, anaerobic methane oxidation coupled with denitrification, and anaerobic ammonium oxidation.
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Affiliation(s)
- Satoshi Ishii
- Division of Environmental Engineering, Hokkaido University, Sapporo, Japan.
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