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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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Kwon Y, Jin Y, Lee JH, Sun C, Ryu CM. Rice rhizobiome engineering for climate change mitigation. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00150-X. [PMID: 39019767 DOI: 10.1016/j.tplants.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/03/2024] [Accepted: 06/17/2024] [Indexed: 07/19/2024]
Abstract
The year 2023 was the warmest year since 1850. Greenhouse gases, including CO2 and methane, played a significant role in increasing global warming. Among these gases, methane has a 25-fold greater impact on global warming than CO2. Methane is emitted during rice cultivation by a group of rice rhizosphere microbes, termed methanogens, in low oxygen (hypoxic) conditions. To reduce methane emissions, it is crucial to decrease the methane production capacity of methanogens through water and fertilizer management, breeding of new rice cultivars, regulating root exudation, and manipulating rhizosphere microbiota. In this opinion article we review the recent developments in hypoxia ecology and methane emission mitigation and propose potential solutions based on the manipulation of microbiota and methanogens for the mitigation of methane emissions.
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Affiliation(s)
- Youngho Kwon
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang, 50441, South Korea
| | - Yunkai Jin
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Jong-Hee Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang, 50441, South Korea
| | - Chuanxin Sun
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea; Department of Pediatrics, University of California at San Diego, La Jolla, CA, 92093-0380, USA.
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3
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Samanta D, Rauniyar S, Saxena P, Sani RK. From genome to evolution: investigating type II methylotrophs using a pangenomic analysis. mSystems 2024; 9:e0024824. [PMID: 38695578 PMCID: PMC11237726 DOI: 10.1128/msystems.00248-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/04/2024] [Indexed: 06/19/2024] Open
Abstract
A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core gene families shared by all 75 organisms, emphasizing their crucial role in the survival and adaptability of these organisms. Additionally, we predicted the functionality of 12 hypothetical proteins. The analysis unveiled a diverse array of genes associated with key metabolic pathways, including methane, serine, glyoxylate, and ethylmalonyl-CoA (EMC) metabolic pathways. While all selected organisms possessed essential genes for the serine pathway, Methylooceanibacter marginalis lacked serine hydroxymethyltransferase (SHMT), and Methylobacterium variabile exhibited both isozymes of SHMT, suggesting its potential to utilize a broader range of carbon sources. Notably, Methylobrevis sp. displayed a unique serine-glyoxylate transaminase isozyme not found in other organisms. Only nine organisms featured anaplerotic enzymes (isocitrate lyase and malate synthase) for the glyoxylate pathway, with the rest following the EMC pathway. Methylovirgula sp. 4MZ18 stood out by acquiring genes from both glyoxylate and EMC pathways, and Methylocapsa sp. S129 featured an A-form malate synthase, unlike the G-form found in the remaining organisms. Our findings also revealed distinct phylogenetic relationships and clustering patterns among type II methylotrophs, leading to the proposal of a separate genus for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129. This pangenomic study unveils remarkable metabolic diversity, unique gene characteristics, and distinct clustering patterns of type II methylotrophs, providing valuable insights for future carbon sequestration and biotechnological applications. IMPORTANCE Methylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity.
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Affiliation(s)
- Dipayan Samanta
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
| | - Shailabh Rauniyar
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
| | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
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Cao W, Zhao J, Cai Y, Mo Y, Ma J, Zhang G, Jiang X, Jia Z. Ridge with no-tillage facilitates microbial N 2 fixation associated with methane oxidation in rice soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171172. [PMID: 38402982 DOI: 10.1016/j.scitotenv.2024.171172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the greenhouse gas methane emission, particularly prevalent in flooded wetlands. The implementation of ridge with no-tillage practices within a rice-rape rotation system proves effective in overcoming the restrictive redox conditions associated with waterlogging. This approach enhances capillary water availability from furrows, especially during periods of low rainfall, thereby supporting plant growth on the ridges. However, the microbe-mediated accumulation of soil organic carbon and nitrogen remains insufficiently understood under this agricultural practice, particularly concerning methane oxidation, which holds ecological and agricultural significance in the rice fields. In this study, the ridge and ditch soils from a 28-year-old ridge with no-tillage rice field experiment were utilized for incubation with 13C-CH4 and 15NN2 to estimate the methane-oxidizing and N2-fixing potentials. Our findings reveal a significantly higher net production of fresh soil organic carbon in the ridge compared to the ditch soil during methane oxidation, with values of 626 and 543 μg 13C g-1 dry weight soil, respectively. Additionally, the fixed 15N exhibited a twofold increase in the ridge soil (14.1 μg 15N g-1 dry weight soil) compared to the ditch soil. Interestingly, the result of DNA-based stable isotope probing indicated no significant differences in active MOB and N2 fixers between ridge and ditch soils. Both Methylocystis-like type II and Methylosarcina/Methylomonas-like type I MOB catalyzed methane into organic biomass carbon pools. Soil N2-fixing activity was associated with the 15N-labeling of methane oxidizers and non-MOB, such as methanol oxidizers (Hyphomicrobium) and conventional N2 fixers (Burkholderia). Methane oxidation also fostered microbial interactions, as evidenced by co-occurrence patterns. These results underscore the dual role of microbial methane oxidation - not only as a recognized sink for the potent greenhouse gas methane but also as a source of soil organic carbon and bioavailable nitrogen. This emphasizes the pivotal role of microbial methane metabolism in contributing to soil carbon and nitrogen accumulation in ridge with no-tillage systems.
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Affiliation(s)
- Weiwei Cao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; Institute for Food and Agricultural Sciences (IFAS), Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, USA
| | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Yongliang Mo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Environmental Science and Engineering, China West Normal University, Nanchong 637002, PR China
| | - Jingjing Ma
- Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun 130102, PR China
| | - Guangbin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xianjun Jiang
- College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun 130102, PR China.
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Minamisawa K. Mitigation of greenhouse gas emission by nitrogen-fixing bacteria. Biosci Biotechnol Biochem 2022; 87:7-12. [PMID: 36354103 DOI: 10.1093/bbb/zbac177] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022]
Abstract
Chemical nitrogen fixation by the Haber-Bosch method permitted industrial-scale fertilizer production that supported global population growth, but simultaneously released reactive nitrogen into the environment. This minireview highlights the potential for bacterial nitrogen fixation and mitigation of greenhouse gas (GHG) emissions from soybean and rice fields. Nitrous oxide (N2O), a GHG, is mainly emitted from agricultural use of nitrogen fertilizer and symbiotic nitrogen fixation. Some rhizobia have a denitrifying enzyme system that includes an N2O reductase and are able to mitigate N2O emission from the rhizosphere of leguminous plants. Type II methane (CH4)-oxidizing bacteria (methanotrophs) are endophytes in paddy rice roots and fix N2 using CH4 (a GHG) as an energy source, mitigating the emission of CH4 and reducing nitrogen fertilizer usage. Thus, symbiotic nitrogen fixation shows potential for GHG mitigation in soybean and rice fields while simultaneously supporting sustainable agriculture.
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Affiliation(s)
- Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, Japan
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Cao W, Cai Y, Bao Z, Wang S, Yan X, Jia Z. Methanotrophy Alleviates Nitrogen Constraint of Carbon Turnover by Rice Root-Associated Microbiomes. Front Microbiol 2022; 13:885087. [PMID: 35663885 PMCID: PMC9159908 DOI: 10.3389/fmicb.2022.885087] [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: 02/27/2022] [Accepted: 04/21/2022] [Indexed: 11/23/2022] Open
Abstract
The bioavailability of nitrogen constrains primary productivity, and ecosystem stoichiometry implies stimulation of N2 fixation in association with carbon sequestration in hotspots such as paddy soils. In this study, we show that N2 fixation was triggered by methane oxidation and the methanotrophs serve as microbial engines driving the turnover of carbon and nitrogen in rice roots. 15N2-stable isotope probing showed that N2-fixing activity was stimulated 160-fold by CH4 oxidation from 0.27 to 43.3 μmol N g–1 dry weight root biomass, and approximately 42.5% of the fixed N existed in the form of 15N-NH4+ through microbial mineralization. Nitrate amendment almost completely abolished N2 fixation. Ecophysiology flux measurement indicated that methane oxidation-induced N2 fixation contributed only 1.9% of total nitrogen, whereas methanotrophy-primed mineralization accounted for 21.7% of total nitrogen to facilitate root carbon turnover. DNA-based stable isotope probing further indicated that gammaproteobacterial Methylomonas-like methanotrophs dominated N2 fixation in CH4-consuming roots, whereas nitrate addition resulted in the shift of the active population to alphaproteobacterial Methylocystis-like methanotrophs. Co-occurring pattern analysis of active microbial community further suggested that a number of keystone taxa could have played a major role in nitrogen acquisition through root decomposition and N2 fixation to facilitate nutrient cycling while maintaining soil productivity. This study thus highlights the importance of root-associated methanotrophs as both biofilters of greenhouse gas methane and microbial engines of bioavailable nitrogen for rice growth.
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Affiliation(s)
- Weiwei Cao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhihua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China.,Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Shuwei Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
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Ketehouli T, Nguyen Quoc VH, Dong J, Do H, Li X, Wang F. Overview of the roles of calcium sensors in plants’ response to osmotic stress signalling. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:589-599. [PMID: 35339206 DOI: 10.1071/fp22012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Calcium signals serve an important function as secondary messengers between cells in various biological processes due to their robust homeostatic mechanism, maintaining an intracellular free Ca2+ concentration. Plant growth, development, and biotic and abiotic stress are all regulated by Ca2+ signals. Ca2+ binding proteins decode and convey the messages encoded by Ca2+ ions. In the presence of high quantities of Mg2+ and monovalent cations, such sensors bind to Ca2+ ions and modify their conformation in a Ca2+ -dependent manner. Calcium-dependent protein kinases (CPKs), calmodulins (CaMs), and calcineurin B-like proteins are all calcium sensors (CBLs). To transmit Ca2+ signals, CPKs, CBLs, and CaMs interact with target proteins and regulate the expression of their genes. These target proteins may be protein kinases, metabolic enzymes, or cytoskeletal-associated proteins. Beyond its role in plant nutrition as a macroelement and its involvement in the plant cell wall structure, calcium modulates many aspects of development, growth and adaptation to environmental constraints such as drought, salinity and osmotic stresses. This review summarises current knowledge on calcium sensors in plant responses to osmotic stress signalling.
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Affiliation(s)
- Toi Ketehouli
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Viet Hoang Nguyen Quoc
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Jinye Dong
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Hoaithuong Do
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaowei Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Fawei Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
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Cui J, Zhang M, Chen L, Zhang S, Luo Y, Cao W, Zhao J, Wang L, Jia Z, Bao Z. Methanotrophs Contribute to Nitrogen Fixation in Emergent Macrophytes. Front Microbiol 2022; 13:851424. [PMID: 35479617 PMCID: PMC9036440 DOI: 10.3389/fmicb.2022.851424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Root-associated aerobic methanotroph plays an important role in reducing methane emissions from wetlands. In this study, we examined the activity of methane-dependent nitrogen fixation and active nitrogen-fixing bacterial communities on the roots of Typha angustifolia and Scirpus triqueter using a 15N-N2 feeding experiment and a cDNA-based clone library sequence of the nifH gene, respectively. A 15N-N2 feeding experiment showed that the N2 fixation rate of S. triqueter (1.74 μmol h-1 g-1 dry weight) was significantly higther than that of T. angustifolia (0.48 μmol h-1 g-1 dry weight). The presence of CH4 significantly increased the incorporation of 15N-labeled N2 into the roots of both plants, and the rate of CH4-dependent N2 fixation of S. triqueter (5.6 μmol h-1 g-1 dry weight) was fivefold higher than that of T. angustifolia (0.94 μmol h-1 g-1 dry weight). The active root-associated diazotrophic communities differed between the plant species. Diazotrophic Methylosinus of the Methylocystaceae was dominant in S. triqueter, while Rhizobium of the Rhizobiaceae was dominant in T. angustifolia. However, there were no significant differences in the copy numbers of nifH between plant species. These results suggest that N2 fixation was enhanced by the oxidation of CH4 in the roots of macrophytes grown in natural wetlands and that root-associated Methylocystacea, including Methylosinus, contribute to CH4 oxidation-dependent N2 fixation.
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Affiliation(s)
- Jing Cui
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- The High School Affiliated to Minzu University of China, Hohhot, China
| | - Meng Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Linxia Chen
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Shaohua Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ying Luo
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Weiwei Cao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ji Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Lixin Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Zhongjun Jia
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhihua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Reuse, Inner Mongolia University, Hohhot, China
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Sakoda M, Tokida T, Sakai Y, Senoo K, Nishizawa T. Mitigation of Paddy Field Soil Methane Emissions by Betaproteobacterium Azoarcus Inoculation of Rice Seeds. Microbes Environ 2022; 37:ME22052. [PMID: 36517028 PMCID: PMC9763044 DOI: 10.1264/jsme2.me22052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Paddy fields are a major source of atmospheric methane, a greenhouse gas produced by methanogens and consumed by methanotrophs in flooded soil. The inoculation of rice seeds with the bacterium Azoarcus sp. KH32C alters the rice root-associated soil bacterial community composition. The present study investigated the effects of KH32C-inoculated rice cultivation on soil methanogens and methanotrophs involved in methane emissions from a rice paddy field. KH32C-inoculated and non-inoculated rice (cv. Nipponbare) were cultivated in a Japanese rice paddy with and without nitrogen fertilizer. Measurements of methane emissions and soil solution chemical properties revealed increases in methane flux over the waterlogged period with elevations in the concentrations of dissolved methane, dissolved organic carbon, and ferrous iron, which is an indicator of soil reduction levels. Reverse transcription quantitative PCR and amplicon sequencing were used to assess the transcription of the methyl-coenzyme M reductase gene (mcrA) from methanogens and the particulate methane monooxygenase gene (pmoA) from methanotrophs in paddy soil. The results obtained showed not only the transcript copy numbers, but also the compositions of mcrA and pmoA transcripts were related to methane flux. KH32C-inoculated rice cultivation recruited soil methanogens and methanotrophs that suppressed high methane synthesis, increased methane consumption, and decreased methane emissions by 23.5 and 17.2% under non-fertilized and nitrogen-fertilized conditions, respectively, while maintaining rice grain yield. The present study demonstrated the mitigation of paddy field methane emissions arising from the use of KH32C in rice cultivation due to its influence on the compositions of soil methanogen and methanotroph populations.
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Affiliation(s)
- Midori Sakoda
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo 183–8509, Japan
| | - Takeshi Tokida
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Ibaraki 305–8604, Japan
| | - Yoriko Sakai
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Ibaraki 305–8604, Japan
| | - Keishi Senoo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113–8657, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113–8657, Japan
| | - Tomoyasu Nishizawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo 183–8509, Japan,Ibaraki University College of Agriculture, Ibaraki 300–0393, Japan, Corresponding author. E-mail: ; Tel: +81–29–888–8684; Fax: +81–29–888–8525
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Lin Y, Yuan J, Liu D, Kang H, Freeman C, Hu HW, Ye G, Ding W. Divergent responses of wetland methane emissions to elevated atmospheric CO 2 dependent on water table. WATER RESEARCH 2021; 205:117682. [PMID: 34592652 DOI: 10.1016/j.watres.2021.117682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Elevated atmospheric CO2 may have consequences for methane (CH4) emissions from wetlands, yet the magnitude and direction remain unpredictable, because the associated mechanisms have not been fully investigated. Here, we established an in situ macrocosm experiment to compare the effects of elevated CO2 (700 ppm) on the CH4 emissions from two wetlands: an intermittently inundated Calamagrostis angustifolia marsh and a permanently inundated Carex lasiocarpa marsh. The elevated CO2 increased CH4 emissions by 27.6-57.6% in the C. angustifolia marsh, compared to a reduction of 18.7-23.5% in the C. lasiocarpa marsh. The CO2-induced increase in CH4 emissions from the C. angustifolia marsh was paralleled with (1) increased dissolved organic carbon (DOC) released from plant photosynthesis and (2) reduced (rate of) CH4 oxidation due to a putative shift in methanotrophic community composition. In contrast, the CO2-induced decrease in CH4 emissions from the C. lasiocarpa marsh was associated with the increases in soil redox potential and pmoA gene abundance. We synthesized data from worldwide wetland ecosystems, and found that the responses of CH4 emissions to elevated CO2 was determined by the wetland water table levels and associated plant oxygen secretion capacity. In conditions with elevated CO2, plants with a high oxygen secretion capacity suppress CH4 emissions while plants with low oxygen secretion capacity stimulate CH4 emissions; both effects are mediated via a feedback loop involving shifts in activities of methanogens and methanotrophs.
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Affiliation(s)
- Yongxin Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 10049, China; Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Deyan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul 120-749, South Korea
| | - Chris Freeman
- School of Natural Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom
| | - Hang-Wei Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Guiping Ye
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 10049, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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11
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Liu J, Han J, Zhu C, Cao W, Luo Y, Zhang M, Zhang S, Jia Z, Yu R, Zhao J, Bao Z. Elevated Atmospheric CO 2 and Nitrogen Fertilization Affect the Abundance and Community Structure of Rice Root-Associated Nitrogen-Fixing Bacteria. Front Microbiol 2021; 12:628108. [PMID: 33967976 PMCID: PMC8103900 DOI: 10.3389/fmicb.2021.628108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
Elevated atmospheric CO2 (eCO2) results in plant growth and N limitation, yet how root-associated nitrogen-fixing bacterial communities respond to increasing atmospheric CO2 and nitrogen fertilization (eN) during the growth stages of rice is unclear. Using the nifH gene as a molecular marker, we studied the combined effect of eCO2 and eN on the diazotrophic community and abundance at two growth stages in rice (tillering, TI and heading, HI). Quantitative polymerase chain reaction (qPCR) showed that eN had no obvious effect on nifH abundance in rice roots under either ambient CO2 (aCO2) or eCO2 treatment at the TI stage; in contrast, at the HI, nifH copy numbers were increased under eCO2 and decreased under aCO2. For rhizosphere soils, eN significantly reduced the abundance of nifH under both aCO2 and eCO2 treatment at the HI stage. Elevated CO2 significantly increased the nifH abundance in rice roots and rhizosphere soils with nitrogen fertilization, but had no obvious effect without N addition at the HI stage. There was a significant interaction [CO2 × N fertilization] effect on nifH abundance in root zone at the HI stage. In addition, the nifH copy numbers in rice roots were significantly higher at the HI stage than at the TI stage. Sequencing analysis indicated that the root-associated diazotrophic community structure tended to cluster according to the nitrogen fertilization treatment and that Rhizobiales were the dominant diazotrophs in all root samples at the HI stage. Additionally, nitrogen fertilization significantly increased the relative abundance of Methylosinus (Methylocystaceae) under eCO2 treatment, but significantly decreased the relative abundance of Rhizobium (Rhizobiaceae) under aCO2 treatment. Overall, the combined effect of eN and eCO2 stimulates root-associated diazotrophic methane-oxidizing bacteria while inhibits heterotrophic diazotrophs.
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Affiliation(s)
- Jumei Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Reuse, Inner Mongolia University, Hohhot, China
- Chongqing Key Laboratory of Environmental Materials and Remediation Technologies, College of Chemistry and Environmental Engineering, Chongqing University of Arts and Sciences, Chongqing, China
| | - Jingjing Han
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Chunwu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Weiwei Cao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ying Luo
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Meng Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Shaohua Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ruihong Yu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Ji Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Zhihua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Reuse, Inner Mongolia University, Hohhot, China
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12
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Peng X, Xie J, Li W, Xie H, Cai Y, Ding X. Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures. PLoS One 2021; 16:e0246687. [PMID: 33556120 PMCID: PMC7870070 DOI: 10.1371/journal.pone.0246687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/23/2021] [Indexed: 11/18/2022] Open
Abstract
Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.
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Affiliation(s)
- Xiaojue Peng
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Provincial People’s Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Jian Xie
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Wenzhuo Li
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Hongwei Xie
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Yaohui Cai
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Xia Ding
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Provincial People’s Hospital, Nanchang University, Nanchang, Jiangxi, China
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13
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Bhandari A, Sandhu N, Bartholome J, Cao-Hamadoun TV, Ahmadi N, Kumari N, Kumar A. Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel. RICE (NEW YORK, N.Y.) 2020; 13:53. [PMID: 32761553 PMCID: PMC7410978 DOI: 10.1186/s12284-020-00406-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/02/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. RESULTS The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. CONCLUSION These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
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Affiliation(s)
- Aditi Bhandari
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Banasthali Vidyapith, Banasthali, 304022, India
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Jérôme Bartholome
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Tuong-Vi Cao-Hamadoun
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Nourollah Ahmadi
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines.
- IRRI South Asia Regional Centre, Varanasi, 221006, India.
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14
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de la Porte A, Schmidt R, Yergeau É, Constant P. A Gaseous Milieu: Extending the Boundaries of the Rhizosphere. Trends Microbiol 2020; 28:536-542. [PMID: 32544440 DOI: 10.1016/j.tim.2020.02.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/07/2019] [Accepted: 02/24/2020] [Indexed: 11/30/2022]
Abstract
Plant root activities shape microbial community functioning in the soil, making the rhizosphere the epicenter of soil biogeochemical processes. With this opinion article, we argue to rethink the rhizosphere boundaries: as gases can diffuse several centimeters away from the roots into the soil, the portion of soil influenced by root activities is larger than the strictly root-adhering soil. Indeed, gases are key drivers of biogeochemical processes due to their roles as energy sources or communication molecules, which has the potential to modify microbial community structure and functioning. In order to get a more holistic perspective on this key environment, we advocate for interdisciplinarity in rhizosphere research by combining knowledge of soluble compounds with gas dynamics.
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Affiliation(s)
- Anne de la Porte
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, H7V 1B7, Canada; Quebec Center for Biodiversity Sciences (QCBS), Montreal, H3A 1B1, Canada
| | - Ruth Schmidt
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, H7V 1B7, Canada; Quebec Center for Biodiversity Sciences (QCBS), Montreal, H3A 1B1, Canada.
| | - Étienne Yergeau
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, H7V 1B7, Canada; Quebec Center for Biodiversity Sciences (QCBS), Montreal, H3A 1B1, Canada
| | - Philippe Constant
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, H7V 1B7, Canada; Quebec Center for Biodiversity Sciences (QCBS), Montreal, H3A 1B1, Canada
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15
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Diversity of active root-associated methanotrophs of three emergent plants in a eutrophic wetland in northern China. AMB Express 2020; 10:48. [PMID: 32170424 PMCID: PMC7070141 DOI: 10.1186/s13568-020-00984-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 03/03/2020] [Indexed: 02/02/2023] Open
Abstract
Root-associated aerobic methanotrophs play an important role in regulating methane emissions from the wetlands. However, the influences of the plant genotype on root-associated methanotrophic structures, especially on active flora, remain poorly understood. Transcription of the pmoA gene, encoding particulate methane monooxygenase in methanotrophs, was analyzed by reverse transcription PCR (RT-PCR) of mRNA isolated from root samples of three emergent macrophytes, including Phragmites australis, Typha angustifolia, and Schoenoplectus triqueter (syn. Scirpus triqueter L.) from a eutrophic wetland. High-throughput sequencing of pmoA based on DNA and cDNA was used to analyze the methanotrophic community. Sequencing of cDNA pmoA amplicons confirmed that the structure of active methanotrophic was not always consistent with DNA. A type I methanotroph, Methylomonas, was the most active group in P. australis, whereas Methylocystis, a type II methanotroph, was the dominant group in S. triqueter. In T. angustifolia, these two types of methanotroph existed in similar proportions. However, at the DNA level, Methylomonas was predominant in the roots of all three plants. In addition, vegetation type could have a profound impact on root-associated methanotrophic community at both DNA and cDNA levels. These results indicate that members of the genera Methylomonas (type I) and Methylocystis (type II) can significantly contribute to aerobic methane oxidation in a eutrophic wetland.
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Liu JM, Bao ZH, Cao WW, Han JJ, Zhao J, Kang ZZ, Wang LX, Zhao J. Enrichment of Type I Methanotrophs with nirS Genes of Three Emergent Macrophytes in a Eutrophic Wetland in China. Microbes Environ 2020; 35. [PMID: 31969532 PMCID: PMC7104278 DOI: 10.1264/jsme2.me19098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The pmoA gene, encoding particulate methane monooxygenase in methanotrophs, and nirS and nirK genes, encoding bacterial nitrite reductases, were examined in the root and rhizosphere sediment of three common emergent macrophytes (Phragmites australis, Typha angustifolia, and Scirpus triqueter) and unvegetated sediment from eutrophic Wuliangsuhai Lake in China. Sequencing analyses indicated that 334 out of 351 cloned pmoA sequences were phylogenetically the most closely related to type I methanotrophs (Gammaproteobacteria), and Methylomonas denitrificans-like organisms accounted for 44.4% of the total community. In addition, 244 out of 250 cloned nirS gene sequences belonged to type I methanotrophs, and 31.2% of nirS genes were the most closely related to paddy rice soil clone SP-2-12 in Methylomonas of the total community. Three genera of type I methanotrophs, Methylomonas, Methylobacter, and Methylovulum, were common in both pmoA and nirS clone libraries in each sample. A quantitative PCR (qPCR) analysis demonstrated that the copy numbers of the nirS and nirK genes were significantly higher in rhizosphere sediments than in unvegetated sediments in P. australis and T. angustifolia plants. In the same sample, the nirS gene copy number was significantly higher than that of nirK. Furthermore, type I methanotrophs were localized in the root tissues according to catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Thus, nirS-carrying type I methanotrophs were enriched in macrophyte root and rhizosphere sediment and are expected to play important roles in carbon/nitrogen cycles in a eutrophic wetland.
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Affiliation(s)
- Ju-Mei Liu
- College of Life Sciences, Inner Mongolia University.,College of Chemistry and Environmental Engineering, Chongqing Key Laboratory of Environmental Materials & Remediation Technologies, Chongqing University of Arts and Sciences
| | - Zhi-Hua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University.,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University
| | - Wei-Wei Cao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Jing-Jing Han
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Jun Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Zhen-Zhong Kang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Li-Xin Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Ji Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University.,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University
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17
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Uroz S, Courty PE, Oger P. Plant Symbionts Are Engineers of the Plant-Associated Microbiome. TRENDS IN PLANT SCIENCE 2019; 24:905-916. [PMID: 31288964 DOI: 10.1016/j.tplants.2019.06.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/03/2019] [Accepted: 06/07/2019] [Indexed: 05/09/2023]
Abstract
Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.
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Affiliation(s)
- Stephane Uroz
- Institut National de la Recherche Agronomique (INRA) Unité Mixte de Recherche (UMR) 1136, Interactions Arbres-Microorganismes, F-54280, Champenoux, France; Université de Lorraine, UMR 1136, Interactions Arbres-Microorganismes, F-54500 Vandoeuvre-lès-, Nancy, France; INRA Unité de Recherche (UR) 1138, Biogéochimie des Écosystèmes Forestiers, F-54280, Champenoux, France.
| | - Pierre Emmanuel Courty
- Agroécologie, Institut National de la Recherche, Agronomique (INRA), AgroSup Dijon, Centre, National de la Recherche Scientifique (CNRS), Université de Bourgogne, INRA, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Phil Oger
- Université de Lyon, Institut National des Sciences Appliquées (INSA) de Lyon, CNRS UMR, 5240, Villeurbanne, France
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18
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Nada RM, Abo-Hegazy SE, Budran EG, Abogadallah GM. The interaction of genes controlling root traits is required for the developmental acquisition of deep and thick root traits and improving root architecture in response to low water or nitrogen content in rice (Oryza sativa L.) cultivars. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:122-132. [PMID: 31151078 DOI: 10.1016/j.plaphy.2019.05.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Most of the hot spots about rice research are related to roots; increasing rice yield is mainly associated with improving root traits. Understanding phenotype-gene regulation relationship in different rice cultivars can contribute to the genetic improvement of root system. The expression pattern of root genes in moroberekan (deep and thick roots and high root/shoot ratio "R/S") was compared to that in Giza178 and PM12 (numerous but shallow roots) and IR64 (fewer but deeper roots than the latter ones). In contrast to the other genotypes, moroberekan did not cease developing deep and thick roots even after 60 days from sowing, perhaps because of not only the consistent upregulation but also the interaction of root genes. Xylem sap flow was significantly higher even under drought (low water content) in moroberekan. Auxin signaling-related ARF12 and PIN1 genes could play key roles in improving root traits in response to low water or nitrogen content. Their concurrent upregulation was coincided with developing 1) deeper roots in moroberekan under drought, 2) thicker and deeper roots in PM12 under low nitrogen content (LN) and 3) new roots with thicker and deeper characteristics in the four genotypes after root trimming. The upregulation of PIN1 or ARF12 in Giza178 at LN, PM12 at drought or in IR64 under drought or LN did not greatly change the root traits. Hierarchical analysis showed that ARF12 and PIN1 were distantly related, but overlapped with other genes controlling root traits. Overexpression of ARF12 and PIN1 could improve root traits in rice cultivars.
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Affiliation(s)
- Reham M Nada
- Department of Botany and Microbiology, Faculty of Science, Damietta University, New Damietta, 34517, Egypt.
| | - Sara E Abo-Hegazy
- Department of Botany and Microbiology, Faculty of Science, Damietta University, New Damietta, 34517, Egypt
| | - Enas G Budran
- Department of Botany and Microbiology, Faculty of Science, Damietta University, New Damietta, 34517, Egypt
| | - Gaber M Abogadallah
- Department of Botany and Microbiology, Faculty of Science, Damietta University, New Damietta, 34517, Egypt
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19
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Sandhu N, Subedi SR, Singh VK, Sinha P, Kumar S, Singh SP, Ghimire SK, Pandey M, Yadaw RB, Varshney RK, Kumar A. Deciphering the genetic basis of root morphology, nutrient uptake, yield, and yield-related traits in rice under dry direct-seeded cultivation systems. Sci Rep 2019; 9:9334. [PMID: 31249338 PMCID: PMC6597570 DOI: 10.1038/s41598-019-45770-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 06/13/2019] [Indexed: 11/18/2022] Open
Abstract
In the face of global water scarcity, a successful transition of rice cultivation from puddled to dry direct-seeded rice (DDSR) is a future need. A genome-wide association study was performed on a complex mapping population for 39 traits: 9 seedling-establishment traits, 14 root and nutrient-uptake traits, 5 plant morphological traits, 4 lodging resistance traits, and 7 yield and yield-contributing traits. A total of 10 significant marker-trait associations (MTAs) were found along with 25 QTLs associated with 25 traits. The percent phenotypic variance explained by SNPs ranged from 8% to 84%. Grain yield was found to be significantly and positively correlated with seedling-establishment traits, root morphological traits, nutrient uptake-related traits, and grain yield-contributing traits. The genomic colocation of different root morphological traits, nutrient uptake-related traits, and grain-yield-contributing traits further supports the role of root morphological traits in improving nutrient uptake and grain yield under DDSR. The QTLs/candidate genes underlying the significant MTAs were identified. The identified promising progenies carrying these QTLs may serve as potential donors to be exploited in genomics-assisted breeding programs for improving grain yield and adaptability under DDSR.
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Affiliation(s)
- Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines.,Punjab Agricultural University, Ludhiana, India
| | - Sushil Raj Subedi
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines.,Agriculture and Forestry University, Rampur, Chitwan, Nepal.,National Rice Research Program, Hardinath, Nepal
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Pallavi Sinha
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - S P Singh
- Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| | | | - Madhav Pandey
- Agriculture and Forestry University, Rampur, Chitwan, Nepal
| | | | - Rajeev K Varshney
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines.
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20
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Konishi N, Okubo T, Yamaya T, Hayakawa T, Minamisawa K. Nitrate Supply-Dependent Shifts in Communities of Root-Associated Bacteria in Arabidopsis. Microbes Environ 2017; 32:314-323. [PMID: 29187692 PMCID: PMC5745015 DOI: 10.1264/jsme2.me17031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application. The relative abundance of operational taxonomic units of 25.8% was significantly changed by the amount of nitrate supplied. Moreover, at the family level, the relative abundance of several major root-associated bacteria including Burkholderiaceae, Paenibacillaceae, Bradyrhizobiaceae, and Rhizobiaceae markedly fluctuated with the application of nitrate. These results suggest that the application of nitrate strongly affects root-associated bacterial ecosystems in Arabidopsis. Bulk soil bacterial communities were also affected by the application of nitrate; however, these changes were markedly different from those in root-associated bacteria. These results also suggest that nitrate-dependent alterations in root-associated bacterial communities are mainly affected by plant-derived factors in Arabidopsis. T-DNA insertion plant lines of the genes for two transcription factors involved in nitrate signaling in Arabidopsis roots, NLP7 and TCP20, showed similar nitrate-dependent shifts in root-associated bacterial communities from the wild-type, whereas minor differences were observed in root-associated bacteria. Thus, these results indicate that NLP7 and TCP20 are not major regulators of nitrate-dependent bacterial communities in Arabidopsis roots.
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Affiliation(s)
- Noriyuki Konishi
- Graduate School of Agricultural Science, Tohoku University.,Division for Interdisciplinary Advanced Research and Education, Tohoku University
| | - Takashi Okubo
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization
| | - Tomoyuki Yamaya
- Division for Interdisciplinary Advanced Research and Education, Tohoku University
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21
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Lin Y, Liu D, Yuan J, Ye G, Ding W. Methanogenic Community Was Stable in Two Contrasting Freshwater Marshes Exposed to Elevated Atmospheric CO 2. Front Microbiol 2017; 8:932. [PMID: 28596763 PMCID: PMC5442310 DOI: 10.3389/fmicb.2017.00932] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/08/2017] [Indexed: 02/01/2023] Open
Abstract
The effects of elevated atmospheric CO2 concentration on soil microbial communities have been previously recorded. However, limited information is available regarding the response of methanogenic communities to elevated CO2 in freshwater marshes. Using high-throughput sequencing and real-time quantitative PCR, we compared the abundance and community structure of methanogens in different compartments (bulk soil, rhizosphere soil, and roots) of Calamagrostis angustifolia and Carex lasiocarpa growing marshes under ambient (380 ppm) and elevated CO2 (700 ppm) atmospheres. C. lasiocarpa rhizosphere was a hotspot for potential methane production, based on the 10-fold higher abundance of the mcrA genes per dry weight. The two marshes and their compartments were occupied by different methanogenic communities. In the C. lasiocarpa marsh, archaeal family Methanobacteriaceae, Rice Cluster II, and Methanosaetaceae co-dominated in the bulk soil, while Methanobacteriaceae was the exclusively dominant methanogen in the rhizosphere soil and roots. Families Methanosarcinaceae and Methanocellaceae dominated in the bulk soil of C. angustifolia marsh. Conversely, Methanosarcinaceae and Methanocellaceae together with Methanobacteriaceae dominated in the rhizosphere soil and roots, respectively, in the C. angustifolia marsh. Elevated atmospheric CO2 increased plant photosynthesis and belowground biomass of C. lasiocarpa and C. angustifolia marshes. However, it did not significantly change the abundance (based on mcrA qPCR), diversity, or community structure (based on high-throughput sequencing) of methanogens in any of the compartments, irrespective of plant type. Our findings suggest that the population and species of the dominant methanogens had weak responses to elevated atmospheric CO2. However, minor changes in specific methanogenic taxa occurred under elevated atmospheric CO2. Despite minor changes, methanogenic communities in different compartments of two contrasting freshwater marshes were rather stable under elevated atmospheric CO2.
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Affiliation(s)
- Yongxin Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China.,University of the Chinese Academy of SciencesBeijing, China
| | - Deyan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Guiping Ye
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China.,University of the Chinese Academy of SciencesBeijing, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
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22
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Bessette S, Moalic Y, Gautey S, Lesongeur F, Godfroy A, Toffin L. Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic-Anoxic Interface of the Congo Deep-Sea Fan. Front Microbiol 2017; 8:715. [PMID: 28487684 PMCID: PMC5403828 DOI: 10.3389/fmicb.2017.00715] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/06/2017] [Indexed: 11/13/2022] Open
Abstract
Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3-5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic-anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA) genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.
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Affiliation(s)
- Sandrine Bessette
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Yann Moalic
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Sébastien Gautey
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Françoise Lesongeur
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Anne Godfroy
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Laurent Toffin
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
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23
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Ahn JH, Lee SA, Kim JM, Kim MS, Song J, Weon HY. Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices. J Microbiol 2016; 54:724-731. [PMID: 27796926 DOI: 10.1007/s12275-016-6463-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 11/29/2022]
Abstract
Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.
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Affiliation(s)
- Jae-Hyung Ahn
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Jeong Myeong Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Myung-Sook Kim
- Soil and Ferilization Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea.
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24
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Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00932-16. [PMID: 27587832 PMCID: PMC5009989 DOI: 10.1128/genomea.00932-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of Methylosinus sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input.
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25
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Akamatsu A, Shimamoto K, Kawano Y. Crosstalk of Signaling Mechanisms Involved in Host Defense and Symbiosis Against Microorganisms in Rice. Curr Genomics 2016; 17:297-307. [PMID: 27499679 PMCID: PMC4955034 DOI: 10.2174/1389202917666160331201602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 07/21/2015] [Accepted: 07/23/2015] [Indexed: 01/01/2023] Open
Abstract
Rice is one of the most important food crops, feeding about half population in the world. Rice pathogens cause enormous damage to rice production worldwide. In plant immunity research, considerable progress has recently been made in our understanding of the molecular mechanisms underlying microbe-associated molecular pattern (MAMP)-triggered immunity. Using genome sequencing and molecular techniques, a number of new MAMPs and their receptors have been identified in the past two decades. Notably, the mechanisms for chitin perception via the lysine motif (LysM) domain-containing receptor OsCERK1, as well as the mechanisms for bacterial MAMP (e.g. flg22, elf18) perception via the leucine-rich repeat (LRR) domain-containing receptors FLS2 and EFR, have been clarified in rice and Arabidopsis, respectively. In chitin signaling in rice, two direct substrates of OsCERK1, Rac/ROP GTPase guanine nucleotide exchange factor OsRacGEF1 and receptor-like cytoplasmic kinase OsRLCK185, have been identified as components of the OsCERK1 complex and are rapidly phosphorylated by OsCERK1 in response to chitin. Interestingly, OsCERK1 also participates in symbiosis with arbuscular mycorrhizal fungi (AMF) in rice and plays a role in the recognition of short-chitin molecules (CO4/5), which are symbiotic signatures included in AMF germinated spore exudates and induced by synthetic strigolactone. Thus, OsCERK1 contributes to both immunity and symbiotic responses. In this review, we describe recent studies on pathways involved in rice immunity and symbiotic signaling triggered by interactions with microorganisms. In addition, we describe recent advances in genetic engineering by using plant immune receptors and symbiotic microorganisms to enhance disease resistance of rice.
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Affiliation(s)
- Akira Akamatsu
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara,Japan;; Present address: Cell and Developmental Biology, John Innes Centre, Norwich,United Kingdom
| | - Ko Shimamoto
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara,Japan
| | - Yoji Kawano
- Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara,Japan;; Present address: Shanghai Center for Plant Stress Biology, Shanghai,P.R. China;; Kihara Institute for Biological Research, Yokohama,Japan
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26
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Minamisawa K, Imaizumi-Anraku H, Bao Z, Shinoda R, Okubo T, Ikeda S. Are Symbiotic Methanotrophs Key Microbes for N Acquisition in Paddy Rice Root? Microbes Environ 2016; 31:4-10. [PMID: 26960961 PMCID: PMC4791114 DOI: 10.1264/jsme2.me15180] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane–nitrogen (CH4–N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N2 fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of 15N natural abundance in a paddy field experiment. Community analyses also indicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH4 oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH4-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH4 oxidation and N2 fixation).
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27
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Nakagawa T, Imaizumi-Anraku H. Rice arbuscular mycorrhiza as a tool to study the molecular mechanisms of fungal symbiosis and a potential target to increase productivity. RICE (NEW YORK, N.Y.) 2015; 8:32. [PMID: 26516078 PMCID: PMC4626465 DOI: 10.1186/s12284-015-0067-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 10/22/2015] [Indexed: 05/08/2023]
Abstract
Rice (Oryza sativa L.) is a monocot model crop for cereal molecular biology. Following the emergence of molecular genetics of arbuscular mycorrhizal (AM) symbiosis in model legumes in the 1990s, studies on rice genetic resources have considerably contributed to our understanding of the molecular mechanisms and evolution of root intracellular symbioses.In this review, we trace the history of these studies and suggest the potential utility of AM symbiosis for improvement in rice productivity.
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Affiliation(s)
- Tomomi Nakagawa
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Haruko Imaizumi-Anraku
- Division of Plant Sicences, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki, 305-8602, Japan.
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28
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Groten K, Nawaz A, Nguyen NHT, Santhanam R, Baldwin IT. Silencing a key gene of the common symbiosis pathway in Nicotiana attenuata specifically impairs arbuscular mycorrhizal infection without influencing the root-associated microbiome or plant growth. PLANT, CELL & ENVIRONMENT 2015; 38:2398-416. [PMID: 25923645 DOI: 10.1111/pce.12561] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 04/08/2015] [Accepted: 04/16/2015] [Indexed: 06/04/2023]
Abstract
While the biochemical function of calcium and calmodulin-dependent protein kinase (CCaMK) is well studied, and plants impaired in the expression of CCaMK are known not to be infected by arbuscular mycorrhizal fungi (AMF) in glasshouse studies, the whole-plant and ecological consequences of CCaMK silencing are not well understood. Here we show that three independently transformed lines of Nicotiana attenuata plants silenced in CCaMK (irCCaMK) are neither infected by Rhizophagus irregularis in the glasshouse nor by native fungal inoculum in the field. The overall fungal community of field-grown roots did not differ significantly among empty vector (EV) and the transgenic lines, and the bacterial communities only showed minor differences, as revealed by the alpha-diversity parameters of bacterial OTUs, which were higher in EV plants compared with two of the three transformed lines, while beta-diversity parameters did not differ. Furthermore, growth and fitness parameters were similar in the glasshouse and field. Herbivory-inducible and basal levels of salicylic acid, jasmonic acid and abscisic acid did not differ among the genotypes, suggesting that activation of the classical defence pathways are not affected by CCaMK silencing. Based on these results, we conclude that silencing of CCaMK has few, if any, non-target effects.
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Affiliation(s)
- Karin Groten
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ali Nawaz
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Nam H T Nguyen
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Rakesh Santhanam
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
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29
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Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants. Appl Environ Microbiol 2014; 80:5043-52. [PMID: 24928870 DOI: 10.1128/aem.00969-14] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a previous study by our group, CH4 oxidation and N2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH4 oxidation and N2 fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativa Nipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the family Methylocystaceae, including Methylosinus spp. Minor nitrogenase proteins such as Methylocella, Bradyrhizobium, Rhodopseudomonas, and Anaeromyxobacter were also detected. Methane monooxygenase proteins (PmoCBA and MmoXYZCBG) were detected in the same bacterial group of the Methylocystaceae. Because these results indicated that Methylocystaceae members mediate both CH4 oxidation and N2 fixation, we examined their localization in rice tissues by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The methanotrophs were localized around the epidermal cells and vascular cylinder in the root tissues of the field-grown rice plants. Our metaproteomics and CARD-FISH results suggest that CH4 oxidation and N2 fixation are performed mainly by type II methanotrophs of the Methylocystaceae, including Methylosinus spp., inhabiting the vascular bundles and epidermal cells of rice roots.
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