1
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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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2
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Castellano-Hinojosa A, Mora C, Strauss SL. Native Rhizobia Improve Plant Growth, Fix N 2, and Reduce Greenhouse Emissions of Sunnhemp More than Commercial Rhizobia Inoculants in Florida Citrus Orchards. PLANTS (BASEL, SWITZERLAND) 2022; 11:3011. [PMID: 36432740 PMCID: PMC9695096 DOI: 10.3390/plants11223011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Sunnhemp (Crotalaria juncea L.) is an important legume cover crop used in tree cropping systems, where there is increased interest by growers to identify rhizobia to maximize soil nitrogen (N) inputs. We aimed to isolate and identify native rhizobia and compare their capabilities with non-native rhizobia from commercial inoculants to fix atmospheric dinitrogen (N2), produce and reduce nitrous oxide (N2O), and improve plant growth. Phylogenetic analyses of sequences of the 16S rRNA and recA, atpD, and glnII genes showed native rhizobial strains belonged to Rhizobium tropici and the non-native strain to Bradyrhizobium japonicum. Plant nodulation tests, sequencing of nodC and nifH genes, and the acetylene-dependent ethylene production assay confirmed the capacity of all strains to nodulate sunnhemp and fix N2. Inoculation with native rhizobial strains resulted in significant increases in root and shoot weight and total C and N contents in the shoots, and showed greater N2-fixation rates and lower emissions of N2O compared to the non-native rhizobium. Our results suggest that native rhizobia improve plant growth, fix N2, and reduce greenhouse emissions of sunnhemp more than commercial rhizobia inoculants in Florida citrus orchards.
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3
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Symbiotic performance of indigenous soybean bradyrhizobia from the Philippines with soybean (Glycine max [L.] Merill) cultivars harboring different Rj genotypes. Symbiosis 2020. [DOI: 10.1007/s13199-020-00731-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Siqueira AF, Sugawara M, Arashida H, Minamisawa K, Sánchez C. Levels of Periplasmic Nitrate Reductase during Denitrification are Lower in Bradyrhizobium japonicum than in Bradyrhizobium diazoefficiens. Microbes Environ 2020; 35. [PMID: 32554940 PMCID: PMC7511789 DOI: 10.1264/jsme2.me19129] [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] [Indexed: 11/30/2022] Open
Abstract
Soybean plants host endosymbiotic dinitrogen (N2)-fixing bacteria from the genus Bradyrhizobium. Under oxygen-limiting conditions, Bradyrhizobium diazoefficiens and Bradyrhizobium japonicum perform denitrification by sequentially reducing nitrate (NO3–) to nitrous oxide (N2O) or N2. The anaerobic reduction of NO3– to N2O was previously shown to be lower in B. japonicum than in B. diazoefficiens due to impaired periplasmic nitrate reductase (Nap) activity in B. japonicum. We herein demonstrated that impaired Nap activity in B. japonicum was due to low Nap protein levels, which may be related to a decline in the production of FixP and FixO proteins by the cbb3-type oxidase.
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5
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Obando M, Correa-Galeote D, Castellano-Hinojosa A, Gualpa J, Hidalgo A, Alché JD, Bedmar E, Cassán F. Analysis of the denitrification pathway and greenhouse gases emissions in Bradyrhizobium sp. strains used as biofertilizers in South America. J Appl Microbiol 2019; 127:739-749. [PMID: 30803109 DOI: 10.1111/jam.14233] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/11/2019] [Accepted: 02/19/2019] [Indexed: 02/02/2023]
Abstract
AIMS Greenhouse gases are considered as potential atmospheric pollutants, with agriculture being one of the main emission sources. The practice of inoculating soybean seeds with Bradyrhizobium sp. might contribute to nitrous oxide (N2 O) emissions. We analysed this capacity in five of the most used strains of Bradyrhizobium sp. in South America. METHODS AND RESULTS We analysed the denitrification pathway and N2 O production by Bradyrhizobium japonicum E109 and CPAC15, Bradyrhizobium diazoefficiens CPAC7 and B. elkanii SEMIA 587 and SEMIA 5019, both in free-living conditions and in symbiosis with soybean. The in silico analysis indicated the absence of nosZ genes in B. japonicum and the presence of all denitrification genes in B. diazoefficiens strains, as well as the absence of nirK, norC and nosZ genes in B. elkanii. The in planta analysis confirmed N2 O production under saprophytic conditions or symbiosis with soybean root nodules. In the case of symbiosis, up to 26.1 and 18.4 times higher in plants inoculated with SEMIA5019 and E109, respectively, than in those inoculated with USDA110. CONCLUSIONS The strains E109, SEMIA 5019, CPAC15 and SEMIA 587 showed the highest N2 O production both as free-living cells and in symbiotic conditions in comparison with USDA110 and CPAC7, which do have the nosZ gene. Although norC and nosZ could not be identified in silico or in vitro in SEMIA 587 and SEMIA 5019, these strains showed the capacity to produce N2 O in our experimental conditions. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report to analyse and confirm the incomplete denitrification capacity and N2 O production in four of the five most used strains of Bradyrhizobium sp. for soybean inoculation in South America.
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Affiliation(s)
- M Obando
- Laboratorio de Fisiología Vegetal e Interacción Planta-Microorganismo, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - D Correa-Galeote
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - A Castellano-Hinojosa
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - J Gualpa
- Laboratorio de Fisiología Vegetal e Interacción Planta-Microorganismo, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - A Hidalgo
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - J D Alché
- Departamento de Protection Vegetal, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - E Bedmar
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - F Cassán
- Laboratorio de Fisiología Vegetal e Interacción Planta-Microorganismo, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
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6
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Sánchez C, Minamisawa K. Nitrogen Cycling in Soybean Rhizosphere: Sources and Sinks of Nitrous Oxide (N 2O). Front Microbiol 2019; 10:1943. [PMID: 31497007 PMCID: PMC6712156 DOI: 10.3389/fmicb.2019.01943] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/07/2019] [Indexed: 01/29/2023] Open
Abstract
Nitrous oxide (N2O) is the third most important greenhouse gas after carbon dioxide and methane, and a prominent ozone-depleting substance. Agricultural soils are the primary anthropogenic source of N2O because of the constant increase in the use of industrial nitrogen (N) fertilizers. The soybean crop is grown on 6% of the world's arable land, and its production is expected to increase rapidly in the future. In this review, we summarize the current knowledge on N-cycle in the rhizosphere of soybean plants, particularly sources and sinks of N2O. Soybean root nodules are the host of dinitrogen (N2)-fixing bacteria from the genus Bradyrhizobium. Nodule decomposition is the main source of N2O in soybean rhizosphere, where soil organisms mediate the nitrogen transformations that produce N2O. This N2O is either emitted into the atmosphere or further reduced to N2 by the bradyrhizobial N2O reductase (N2OR), encoded by the nos gene cluster. The dominance of nos - indigenous populations of soybean bradyrhizobia results in the emission of N2O into the atmosphere. Hence, inoculation with nos + or nos ++ (mutants with enhanced N2OR activity) bradyrhizobia has proved to be promising strategies to reduce N2O emission in the field. We discussed these strategies, the molecular mechanisms underlying them, and the future perspectives to develop better options for global mitigation of N2O emission from soils.
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Affiliation(s)
- Cristina Sánchez
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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Lin YT, Lin YF, Tsai IJ, Chang EH, Jien SH, Lin YJ, Chiu CY. Structure and Diversity of Soil Bacterial Communities in Offshore Islands. Sci Rep 2019; 9:4689. [PMID: 30894580 PMCID: PMC6426884 DOI: 10.1038/s41598-019-41170-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 03/01/2019] [Indexed: 11/09/2022] Open
Abstract
The effects of biogeographical separation and parent material differences in soil bacterial structure and diversity in offshore islands remain poorly understood. In the current study, we used next-generation sequencing to characterize the differences in soil bacterial communities in five offshore subtropical granite islands (Matsu Islets, MI) of mainland China and two offshore tropical andesite islands (Orchid [OI] and Green Islands [GI]) of Taiwan. The soils of OI and GI were more acidic and had higher organic carbon and total nitrogen content than MI soils. The bacterial communities were dominated by Acidobacteria and Proteobacteria but had different relative abundance because soils were derived from different parent material and because of geographic distance. Non-metric multi-dimensional scaling revealed that the communities formed different clusters among different parent material and geographically distributed soils. The alpha-diversity in bacterial communities was higher in tropical than subtropical soils. Mantel test and redundancy analysis indicated that bacterial diversity and compositions of OI and GI soils, respectively, were positively correlated with soil pH, organic carbon, total nitrogen, microbial biomass carbon and nitrogen. These results suggest that variations in soil properties of offshore islands could result from differences in soil parent material. Distinct soils derived from different parent material and geographic distance could in turn alter the bacterial communities.
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Affiliation(s)
- Yu-Te Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Yu-Fei Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Isheng J Tsai
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Ed-Haun Chang
- Mackay Junior College of Medicine, Nursing and Management, Beitou, Taipei, 11260, Taiwan
| | - Shih-Hao Jien
- Department of Soil and Water Conservation, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan
| | - Yen-Ju Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
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8
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Mason MLT, Tabing BLC, Yamamoto A, Saeki Y. Influence of flooding and soil properties on the genetic diversity and distribution of indigenous soybean-nodulating bradyrhizobia in the Philippines. Heliyon 2018; 4:e00921. [PMID: 30480155 PMCID: PMC6240709 DOI: 10.1016/j.heliyon.2018.e00921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/03/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022] Open
Abstract
One of the strategies that is commonly used in the Philippines to improve the production of soybean is by inoculation. However, this technique often fails mainly due to the lack of information about the indigenous soybean rhizobia in the Philippines soil. In this study, the diversity of indigenous bradyrhizobia collected from the non-flooded and flooded soil conditions at 11 locations in the country was investigated using a local soybean cultivar as the host plant. The genetic variation among the 424 isolates was detected through Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) treatment and sequence analysis for 16S rRNA gene, 16S-23S rRNA internal transcribed spacer (ITS) region and rpoB housekeeping gene. All the isolates were classified under the Bradyrhizobium species namely B. elkanii, B. diazoefficiens, B. japonicum, B. yuanmingense and a considerable proportion of the isolates were clustered under Bradyrhizobium sp. The isolates which were classified under Bradyrhizobium sp. were thought to be endemic to Philippines soil as evidenced by their nucleotide divergence against the known rhizobia and the historical absence of rhizobia inoculation in the collection sites. The major influence on the distribution and diversity of soybean bradyrhizobia is attributed to the difference in the flooding period, followed by soil properties such as pH, soil type, and nutrient content. As determined, it is proposed that the major micro-symbiont of soybean in the Philippines are B. elkanii for non-flooded soils, then B. diazoefficiens and B. japonicum for flooded soils.
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Affiliation(s)
- Maria Luisa Tabing Mason
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Gakuenkibanadai Nishi, Miyazaki, Japan.,College of Agriculture, Central Luzon State University, Science City of Muñoz, Nueva Ecija, Philippines
| | - Baby Lyn Cortez Tabing
- College of Agriculture, Don Mariano Marcos Memorial State University-South Luzon Campus, Rosario, La Union, Philippines
| | - Akihiro Yamamoto
- Faculty of Agriculture, University of Miyazaki, Gakuenkibanadai Nishi, Miyazaki, Japan
| | - Yuichi Saeki
- Faculty of Agriculture, University of Miyazaki, Gakuenkibanadai Nishi, Miyazaki, Japan
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9
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Jang J, Ashida N, Kai A, Isobe K, Nishizawa T, Otsuka S, Yokota A, Senoo K, Ishii S. Presence of Cu-Type (NirK) and cd 1-Type (NirS) Nitrite Reductase Genes in the Denitrifying Bacterium Bradyrhizobium nitroreducens sp. nov. Microbes Environ 2018; 33:326-331. [PMID: 30158366 PMCID: PMC6167111 DOI: 10.1264/jsme2.me18039] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nitrite reductase is a key enzyme for denitrification. There are two types of nitrite reductases: copper-containing NirK and cytochrome cd1-containing NirS. Most denitrifiers possess either nirK or nirS, although a few strains been reported to possess both genes. We herein report the presence of nirK and nirS in the soil-denitrifying bacterium Bradyrhizobium sp. strain TSA1T. Both nirK and nirS were identified and actively transcribed under denitrification conditions. Based on physiological, chemotaxonomic, and genomic properties, strain TSA1T (=JCM 18858T=KCTC 62391T) represents a novel species within the genus Bradyrhizobium, for which we propose the name Bradyrhizobium nitroreducens sp. nov.
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Affiliation(s)
| | - Naoaki Ashida
- Department of Applied Biological Chemistry, The University of Tokyo
| | - Ayaaki Kai
- Department of Applied Biological Chemistry, The University of Tokyo
| | - Kazuo Isobe
- Department of Applied Biological Chemistry, The University of Tokyo
| | - Tomoyasu Nishizawa
- Department of Food and Life Sciences, Ibaraki University College of Agriculture
| | - Shigeto Otsuka
- Department of Applied Biological Chemistry, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Akira Yokota
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo.,Division of Bioscience and Biotechnology for Future Bioindustries, Graduate School of Agricultural Sciences, Tohoku University
| | - Keishi Senoo
- Department of Applied Biological Chemistry, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Satoshi Ishii
- Biotechnology Institute, University of Minnesota.,Department of Soil, Water, and Climate, University of Minnesota
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10
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Duangkhet M, Chikoti Y, Thepsukhon A, Thapanapongworakul P, Chungopast S, Tajima S, Nomura M. Isolation and characterization of rhizobia from nodules of Clitoria ternatea in Thailand. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:123-129. [PMID: 31819714 PMCID: PMC6879394 DOI: 10.5511/plantbiotechnology.18.0402a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/02/2018] [Indexed: 05/28/2023]
Abstract
Rhizobia were isolated from the root nodules of Clitoria ternatea in Thailand. The phylogeny of the isolates was investigated using 16S rDNA and the internal transcribed spacer (ITS) region from 16S to 23S rDNA. The phylogenetic tree of the 16S rDNA showed that ten of the eleven isolates belonged to Bradyrhizobium elkanii, and one belonged to Bradyrhizobium japonicum. The topology of the ITS tree was similar to that of 16S rDNA. The acetylene reduction activity was higher for the nodules inoculated with the isolated B. elkanii strains than for those inoculated with B. japonicum strains. When C. ternatea plants were inoculated with various Bradyrhizobium USDA strains isolated from Glycine max, C. ternatea formed many effective nodules with B. elkanii, especially USDA61. However, acetylene reduction activity per plant and the growth were higher in C. ternatea inoculated with our isolates. From these data we propose that effective rhizobia inoculant were identified for C. ternatea cultivation.
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Affiliation(s)
- Mallika Duangkhet
- Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Yamikani Chikoti
- Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Apiraya Thepsukhon
- Faculty of Agricultural Production, Maejo University, Chiang Mai, 50290, Thailand
| | | | - Sirinapa Chungopast
- Faculty of Agriculture Kamphaeng-saen, Kasetsart University, Nakorn Pathom 73140, Thailand
| | - Shigeyuki Tajima
- Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Mika Nomura
- Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
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11
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Sánchez C, Minamisawa K. Redundant roles of Bradyrhizobium oligotrophicum Cu-type (NirK) and cd1-type (NirS) nitrite reductase genes under denitrifying conditions. FEMS Microbiol Lett 2018; 365:4817536. [DOI: 10.1093/femsle/fny015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/18/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Cristina Sánchez
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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12
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Siqueira AF, Minamisawa K, Sánchez C. Anaerobic Reduction of Nitrate to Nitrous Oxide Is Lower in Bradyrhizobium japonicum than in Bradyrhizobium diazoefficiens. Microbes Environ 2017; 32:398-401. [PMID: 29109361 PMCID: PMC5745027 DOI: 10.1264/jsme2.me17081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
When soil oxygen levels decrease, some bradyrhizobia use denitrification as an alternative form of respiration. Bradyrhizobium diazoefficiens (nos+) completely denitrifies nitrate (NO3-) to dinitrogen, whereas B. japonicum (nos-) is unable to reduce nitrous oxide to dinitrogen. We found that anaerobic growth with NO3- as the electron acceptor was significantly lower in B. japonicum than in B. diazoefficiens, and this was not explained by the absence of nos in B. japonicum. Our results indicate that the reason for the limited growth of B. japonicum is weak NO3- reduction due to impaired periplasmic nitrate reductase activity, which may rely on posttranscriptional events.
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13
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Saeki Y, Nakamura M, Mason MLT, Yano T, Shiro S, Sameshima-Saito R, Itakura M, Minamisawa K, Yamamoto A. Effect of Flooding and the nosZ Gene in Bradyrhizobia on Bradyrhizobial Community Structure in the Soil. Microbes Environ 2017; 32:154-163. [PMID: 28592720 PMCID: PMC5478539 DOI: 10.1264/jsme2.me16132] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 04/11/2017] [Indexed: 11/12/2022] Open
Abstract
We investigated the effects of the water status (flooded or non-flooded) and presence of the nosZ gene in bradyrhizobia on the bradyrhizobial community structure in a factorial experiment that examined three temperature levels (20°C, 25°C, and 30°C) and two soil types (andosol and gray lowland soil) using microcosm incubations. All microcosms were inoculated with Bradyrhizobium japonicum USDA6T, B. japonicum USDA123, and B. elkanii USDA76T, which do not possess the nosZ gene, and then half received B. diazoefficiens USDA110Twt (wt for the wild-type) and the other half received B. diazoefficiens USDA110ΔnosZ. USDA110Twt possesses the nosZ gene, which encodes N2O reductase; 110ΔnosZ, a mutant variant, does not. Changes in the community structure after 30- and 60-d incubations were investigated by denaturing-gradient gel electrophoresis and an image analysis. USDA6T and 76T strains slightly increased in non-flooded soil regardless of which USDA110T strain was present. In flooded microcosms with the USDA110Twt strain, USDA110Twt became dominant, whereas in microcosms with the USDA110ΔnosZ, a similar change in the community structure occurred to that in non-flooded microcosms. These results suggest that possession of the nosZ gene confers a competitive advantage to B. diazoefficiens USDA110T in flooded soil. We herein demonstrated that the dominance of B. diazoefficiens USDA110Twt within the soil bradyrhizobial population may be enhanced by periods of flooding or waterlogging systems such as paddy-soybean rotations because it appears to have the ability to thrive in moderately anaerobic soil.
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Affiliation(s)
- Yuichi Saeki
- Faculty of Agriculture, University of MiyazakiMiyazaki 889–2192Japan
| | - Misato Nakamura
- Faculty of Agriculture, University of MiyazakiMiyazaki 889–2192Japan
| | - Maria Luisa T. Mason
- Faculty of Agriculture, University of MiyazakiMiyazaki 889–2192Japan
- College of Agriculture, Central Luzon State UniversityScience City of Muñoz, 3120 Nueva EcijaPhilippines
| | - Tsubasa Yano
- Faculty of Agriculture, University of MiyazakiMiyazaki 889–2192Japan
| | - Sokichi Shiro
- Faculty of Life and Environmental Science, Shimane UniversityShimane 690–8504Japan
| | - Reiko Sameshima-Saito
- College of Agriculture, Academic Institute, Shizuoka UniversityShizuoka 422–8529Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku UniversitySendai, Miyagi 980–8577Japan
- Center for Ecological Evolutionary Developmental Biology, Kyoto Sangyo UniversityKyoto 603–8555Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku UniversitySendai, Miyagi 980–8577Japan
| | - Akihiro Yamamoto
- Faculty of Agriculture, University of MiyazakiMiyazaki 889–2192Japan
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14
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Akiyama H, Hoshino YT, Itakura M, Shimomura Y, Wang Y, Yamamoto A, Tago K, Nakajima Y, Minamisawa K, Hayatsu M. Mitigation of soil N2O emission by inoculation with a mixed culture of indigenous Bradyrhizobium diazoefficiens. Sci Rep 2016; 6:32869. [PMID: 27633524 PMCID: PMC5025649 DOI: 10.1038/srep32869] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/11/2016] [Indexed: 11/11/2022] Open
Abstract
Agricultural soil is the largest source of nitrous oxide (N2O), a greenhouse gas. Soybean is an important leguminous crop worldwide. Soybean hosts symbiotic nitrogen-fixing soil bacteria (rhizobia) in root nodules. In soybean ecosystems, N2O emissions often increase during decomposition of the root nodules. Our previous study showed that N2O reductase can be used to mitigate N2O emission from soybean fields during nodule decomposition by inoculation with nosZ++ strains [mutants with increased N2O reductase (N2OR) activity] of Bradyrhizobium diazoefficiens. Here, we show that N2O emission can be reduced at the field scale by inoculation with a mixed culture of indigenous nosZ+ strains of B. diazoefficiens USDA110 group isolated from Japanese agricultural fields. Our results also suggested that nodule nitrogen is the main source of N2O production during nodule decomposition. Isolating nosZ+ strains from local soybean fields would be more applicable and feasible for many soybean-producing countries than generating mutants.
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Affiliation(s)
- Hiroko Akiyama
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Yuko Takada Hoshino
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yumi Shimomura
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Yong Wang
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Akinori Yamamoto
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Yasuhiro Nakajima
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki 305-8604, Japan
- Advanced Analysis Center, NARO, 3-1-3, Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki 305-8604, Japan
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15
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Shiina Y, Itakura M, Choi H, Saeki Y, Hayatsu M, Minamisawa K. Relationship between soil type and N₂O reductase genotype (nosZ) of indigenous soybean bradyrhizobia: nosZ-minus populations are dominant in Andosols. Microbes Environ 2014; 29:420-6. [PMID: 25476067 PMCID: PMC4262367 DOI: 10.1264/jsme2.me14130] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/14/2014] [Indexed: 11/29/2022] Open
Abstract
Bradyrhizobium japonicum strains that have the nosZ gene, which encodes N2O reductase, are able to mitigate N2O emissions from soils (15). To examine the distribution of nosZ genotypes among Japanese indigenous soybean bradyrhizobia, we isolated bradyrhizobia from the root nodules of soybean plants inoculated with 32 different soils and analyzed their nosZ and nodC genotypes. The 1556 resultant isolates were classified into the nosZ+/nodC+ genotype (855 isolates) and nosZ-/nodC+ genotype (701 isolates). The 11 soil samples in which nosZ- isolates significantly dominated (P < 0.05; the χ(2) test) were all Andosols (a volcanic ash soil prevalent in agricultural fields in Japan), whereas the 17 soil samples in which nosZ+ isolates significantly dominated were mainly alluvial soils (non-volcanic ash soils). This result was supported by a principal component analysis of environmental factors: the dominance of the nosZ- genotype was positively correlated with total N, total C, and the phosphate absorption coefficient in the soils, which are soil properties typical of Andosols. Internal transcribed spacer sequencing of representative isolates showed that the nosZ+ and nosZ- isolates of B. japonicum fell mainly into the USDA110 (BJ1) and USDA6 (BJ2) groups, respectively. These results demonstrated that the group lacking nosZ was dominant in Andosols, which can be a target soil type for an N2O mitigation strategy in soybean fields. We herein discussed how the nosZ genotypes of soybean bradyrhizobia depended on soil types in terms of N2O respiration selection and genomic determinants for soil adaptation.
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Affiliation(s)
- Yoko Shiina
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Hyunseok Choi
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Yuichi Saeki
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, Miyazaki University, Miyazaki 889–2192,
Japan
| | - Masahito Hayatsu
- National Institute for Agro-Environmental Sciences, 3–1–3, Kannondai, Tsukuba, Ibaraki 305–8604,
Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
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16
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Genome analysis suggests that the soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica. Appl Environ Microbiol 2013; 79:2542-51. [PMID: 23396330 DOI: 10.1128/aem.00009-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agromonas oligotrophica (Bradyrhizobium oligotrophicum) S58(T) is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lacking nodABC genes and the typical symbiosis island. The genome showed a high level of similarity to the genomes of Bradyrhizobium sp. ORS278 and Bradyrhizobium sp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant, Aeschynomene indica, in a Nod factor-independent manner. Although nonsymbiotic (brady)rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nif and fix) with A. indica were well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with five A. oligotrophica strains (S58, S42, S55, S72, and S80). Surprisingly, all five strains of A. oligotrophica formed effective nitrogen-fixing nodules on the roots and/or stems of A. indica, with differentiated bacteroids. Nonsymbiotic (brady)rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwelling A. oligotrophica generally possesses the ability to establish symbiosis with A. indica. Phylogenetic analyses suggest that Nod factor-independent symbiosis with A. indica is a common trait of nodABC- and symbiosis island-lacking strains within the members of the photosynthetic Bradyrhizobium clade, including A. oligotrophica.
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17
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Inaba S, Ikenishi F, Itakura M, Kikuchi M, Eda S, Chiba N, Katsuyama C, Suwa Y, Mitsui H, Minamisawa K. N(2)O emission from degraded soybean nodules depends on denitrification by Bradyrhizobium japonicum and other microbes in the rhizosphere. Microbes Environ 2012; 27:470-6. [PMID: 23047151 PMCID: PMC4103556 DOI: 10.1264/jsme2.me12100] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 05/30/2012] [Indexed: 11/12/2022] Open
Abstract
A model system developed to produce N(2)O emissions from degrading soybean nodules in the laboratory was used to clarify the mechanism of N(2)O emission from soybean fields. Soybean plants inoculated with nosZ-defective strains of Bradyrhizobium japonicum USDA110 (ΔnosZ, lacking N(2)O reductase) were grown in aseptic jars. After 30 days, shoot decapitation (D, to promote nodule degradation), soil addition (S, to supply soil microbes), or both (DS) were applied. N(2)O was emitted only with DS treatment. Thus, both soil microbes and nodule degradation are required for the emission of N(2)O from the soybean rhizosphere. The N(2)O flux peaked 15 days after DS treatment. Nitrate addition markedly enhanced N(2)O emission. A (15)N tracer experiment indicated that N(2)O was derived from N fixed in the nodules. To evaluate the contribution of bradyrhizobia, N(2)O emission was compared between a nirK mutant (ΔnirKΔnosZ, lacking nitrite reductase) and ΔnosZ. The N(2)O flux from the ΔnirKΔnosZ rhizosphere was significantly lower than that from ΔnosZ, but was still 40% to 60% of that of ΔnosZ, suggesting that N(2)O emission is due to both B. japonicum and other soil microorganisms. Only nosZ-competent B. japonicum (nosZ+ strain) could take up N(2)O. Therefore, during nodule degradation, both B. japonicum and other soil microorganisms release N(2)O from nodule N via their denitrification processes (N(2)O source), whereas nosZ-competent B. japonicum exclusively takes up N(2)O (N(2)O sink). Net N(2)O flux from soybean rhizosphere is likely determined by the balance of N(2)O source and sink.
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Affiliation(s)
- Shoko Inaba
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Fumio Ikenishi
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Masakazu Kikuchi
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Shima Eda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Naohiko Chiba
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1–13–27 Kasuga, Bunkyo-ku, Tokyo 112–8551,
Japan
| | - Chie Katsuyama
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1–13–27 Kasuga, Bunkyo-ku, Tokyo 112–8551,
Japan
| | - Yuichi Suwa
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1–13–27 Kasuga, Bunkyo-ku, Tokyo 112–8551,
Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
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18
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Shiro S, Yamamoto A, Umehara Y, Hayashi M, Yoshida N, Nishiwaki A, Yamakawa T, Saeki Y. Effect of Rj genotype and cultivation temperature on the community structure of soybean-nodulating bradyrhizobia. Appl Environ Microbiol 2012; 78:1243-50. [PMID: 22156423 PMCID: PMC3272988 DOI: 10.1128/aem.06239-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 11/29/2011] [Indexed: 11/20/2022] Open
Abstract
The nodulation tendency and community structure of indigenous bradyrhizobia on Rj genotype soybean cultivars at cultivation temperatures of 33/28°C, 28/23°C, and 23/18°C for 16/8 h (day/night degrees, hours) were investigated using 780 bradyrhizobial DNA samples from an Andosol with 13 soybean cultivars of four Rj genotypes (non-Rj, Rj(2)Rj(3), Rj(4), and Rj(2)Rj(3)Rj(4)). A dendrogram was constructed based on restriction fragment length polymorphism of the PCR products (PCR-RFLP) of the 16S-23S rRNA gene internal transcribed spacer region. Eleven Bradyrhizobium U.S. Department of Agriculture strains were used as a reference. The dendrogram indicated seven clusters based on similarities among the reference strains. The occupancy rate of the Bj123 cluster decreased with increasing cultivation temperature, whereas the occupancy rates of the Bj110 cluster, Be76 cluster, and Be94 cluster increased with increasing cultivation temperature. In particular, the Rj(2)Rj(3)Rj(4) genotype soybeans were infected with a number of Bj110 clusters, regardless of the increasing cultivation temperature, compared to other Rj genotype soybean cultivars. The ratio of beta diversity to gamma diversity (H'(β)/H'(γ)), which represents differences in the bradyrhizobial communities by pairwise comparison among cultivation temperature sets within the same soybean cultivar, indicated that the bradyrhizobial communities tended to be different among cultivation temperatures. Multidimensional scaling analysis indicated that the infection of the Bj110 cluster and the Bj123 cluster by host soybean genotype and the cultivation temperature affected the bradyrhizobial communities. These results suggested that the Rj genotypes and cultivation temperatures affected the nodulation tendency and community structures of soybean-nodulating bradyrhizobia.
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Affiliation(s)
- Sokichi Shiro
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Japan
| | | | - Yosuke Umehara
- National Institute of Agrobiological Sciences, Ibaraki, Japan
| | - Masaki Hayashi
- National Institute of Agrobiological Sciences, Ibaraki, Japan
| | - Naoto Yoshida
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Aya Nishiwaki
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Takeo Yamakawa
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yuichi Saeki
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
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19
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Hirayama J, Eda S, Mitsui H, Minamisawa K. Nitrate-dependent N₂O emission from intact soybean nodules via denitrification by Bradyrhizobium japonicum bacteroids. Appl Environ Microbiol 2011; 77:8787-90. [PMID: 22003029 PMCID: PMC3233077 DOI: 10.1128/aem.06262-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 10/10/2011] [Indexed: 11/20/2022] Open
Abstract
In the presence of nitrate, N₂O emission increased markedly from soybean roots inoculated with nosZ mutant of Bradyrhizobium japonicum, but not from soybean roots inoculated with a napA nosZ double mutant, indicating that B. japonicum bacteroids in soybean nodules are able to convert the exogenously supplied nitrate into N₂O via a denitrification pathway.
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Affiliation(s)
- Junta Hirayama
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shima Eda
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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20
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Ryuda N, Hashimoto T, Ueno D, Inoue K, Someya T. Visualization and direct counting of individual denitrifying bacterial cells in soil by nirK-targeted direct in situ PCR. Microbes Environ 2011; 26:74-80. [PMID: 21487206 DOI: 10.1264/jsme2.me10180] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The abundance of denitrifying bacteria in soil has been determined primarily by the conventional most probable number (MPN) method. We have developed a single-cell identification technique that is culture-independent, direct in situ PCR, to enumerate denitrifying bacteria in soils. The specificity of this method was evaluated with six species of denitrifying bacteria using nirK as the target gene; Escherichia coli was used as a negative control. Almost all (97.3%-100%) of the nirK-type denitrifying bacteria (Agromonas oligotrophica, Alcaligenes faecalis, Achromobacter denitrificans, Bradyrhizobium japonicum, and Pseudomonas chlororaphis) were detected by direct in situ PCR, whereas no E. coli cells and only a few cells (2.4%) of nirS-type denitrifying bacteria (Pseudomonas aeruginosa) were detected. Numbers of denitrifying bacteria in upland and paddy soil samples quantified by this method were 3.3 × 10(8) to 2.6 × 10(9) cells g(-1) dry soil. These values are approximately 1,000 to 300,000 times higher than those estimated by the MPN method. These results suggest that direct in situ PCR is a better tool for quantifying denitrifying bacteria in soil than the conventional MPN method.
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Affiliation(s)
- Noriko Ryuda
- Division of Soil Science, Faculty of Agriculture, Saga University, Saga 840–8502, Japan
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21
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Ishii S, Ohno H, Tsuboi M, Otsuka S, Senoo K. Identification and isolation of active N2O reducers in rice paddy soil. ISME JOURNAL 2011; 5:1936-45. [PMID: 21677691 DOI: 10.1038/ismej.2011.69] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Dissolved N(2)O is occasionally detected in surface and ground water in rice paddy fields, whereas little or no N(2)O is emitted to the atmosphere above these fields. This indicates the occurrence of N(2)O reduction in rice paddy fields; however, identity of the N(2)O reducers is largely unknown. In this study, we employed both culture-dependent and culture-independent approaches to identify N(2)O reducers in rice paddy soil. In a soil microcosm, N(2)O and succinate were added as the electron acceptor and donor, respectively, for N(2)O reduction. For the stable isotope probing (SIP) experiment, (13)C-labeled succinate was used to identify succinate-assimilating microbes under N(2)O-reducing conditions. DNA was extracted 24 h after incubation, and heavy and light DNA fractions were separated by density gradient ultracentrifugation. Denaturing gradient gel electrophoresis and clone library analysis targeting the 16S rRNA and the N(2)O reductase gene were performed. For culture-dependent analysis, the microbes that elongated under N(2)O-reducing conditions in the presence of cell-division inhibitors were individually captured by a micromanipulator and transferred to a low-nutrient medium. The N(2)O-reducing ability of these strains was examined by gas chromatography/mass spectrometry. Results of the SIP analysis suggested that Burkholderiales and Rhodospirillales bacteria dominated the population under N(2)O-reducing conditions, in contrast to the control sample (soil incubated with only (13)C-succinate). Results of the single-cell isolation technique also indicated that the majority of the N(2)O-reducing strains belonged to the genera Herbaspirillum (Burkholderiales) and Azospirillum (Rhodospirillales). In addition, Herbaspirillum strains reduced N(2)O faster than Azospirillum strains. These results suggest that Herbaspirillum spp. may have an important role in N(2)O reduction in rice paddy soils.
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Affiliation(s)
- Satoshi Ishii
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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22
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Isolation of oligotrophic denitrifiers carrying previously uncharacterized functional gene sequences. Appl Environ Microbiol 2010; 77:338-42. [PMID: 21075882 DOI: 10.1128/aem.02189-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oligotrophic denitrifying bacteria, including those belonging to the genera Herbaspirillum, Azospirillum, and Bradyrhizobium, were obtained using a single-cell isolation technique. The taxonomic composition of the denitrifier population was similar to those assessed by previous culture-independent studies. The sequencing of nitrite reductase and N(2)O reductase genes of these strains revealed previously unknown links between 16S rRNA and the denitrification-functional gene phylogenies. In particular, we identified Bradyrhizobium strains that harbor nirS sequences previously detected only in culture-independent studies.
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23
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Thiosulfate-dependent chemolithoautotrophic growth of Bradyrhizobium japonicum. Appl Environ Microbiol 2010; 76:2402-9. [PMID: 20173070 DOI: 10.1128/aem.02783-09] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thiosulfate-oxidizing sox gene homologues were found at four loci (I, II, III, and IV) on the genome of Bradyrhizobium japonicum USDA110, a symbiotic nitrogen-fixing bacterium in soil. In fact, B. japonicum USDA110 can oxidize thiosulfate and grow under a chemolithotrophic condition. The deletion mutation of the soxY(1) gene at the sox locus I, homologous to the sulfur-oxidizing (Sox) system in Alphaproteobacteria, left B. japonicum unable to oxidize thiosulfate and grow under chemolithotrophic conditions, whereas the deletion mutation of the soxY(2) gene at sox locus II, homologous to the Sox system in green sulfur bacteria, produced phenotypes similar to those of wild-type USDA110. Thiosulfate-dependent O(2) respiration was observed only in USDA110 and the soxY(2) mutant and not in the soxY(1) mutant. In the cells, 1 mol of thiosulfate was stoichiometrically converted to approximately 2 mol of sulfate and consumed approximately 2 mol of O(2). B. japonicum USDA110 showed (14)CO(2) fixation under chemolithotrophic growth conditions. The CO(2) fixation of resting cells was significantly dependent on thiosulfate addition. These results show that USDA110 is able to grow chemolithoautotrophically using thiosulfate as an electron donor, oxygen as an electron acceptor, and carbon dioxide as a carbon source, which likely depends on sox locus I including the soxY(1) gene on USDA110 genome. Thiosulfate oxidation capability is frequently found in members of the Bradyrhizobiaceae, which phylogenetic analysis showed to be associated with the presence of sox locus I homologues, including the soxY(1) gene of B. japonicum USDA110.
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24
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Sudtachat N, Ito N, Itakura M, Masuda S, Eda S, Mitsui H, Kawaharada Y, Minamisawa K. Aerobic vanillate degradation and C1 compound metabolism in Bradyrhizobium japonicum. Appl Environ Microbiol 2009; 75:5012-7. [PMID: 19502448 PMCID: PMC2725485 DOI: 10.1128/aem.00755-09] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 05/27/2009] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium japonicum, a symbiotic nitrogen-fixing soil bacterium, has multiple gene copies for aromatic degradation on the genome and is able to use low concentrations of vanillate, a methoxylated lignin monomer, as an energy source. A transcriptome analysis indicated that one set of vanA1B, pcaG1H1, and genes for C(1) compound catabolism was upregulated in B. japonicum USDA110 cells grown in vanillate (N. Ito, M. Itakura, S. Eda, K. Saeki, H. Oomori, T. Yokoyama, T. Kaneko, S. Tabata, T. Ohwada, S. Tajima, T. Uchiumi, E. Masai, M. Tsuda, H. Mitsui, and K. Minamisawa, Microbes Environ. 21:240-250, 2006). To examine the functions of these genes in vanillate degradation, we tested cell growth and substrate consumption in vanA1B, pcaG1H1, and mxaF mutants of USDA110. The vanA1B and pcaG1H1 mutants were unable to grow in minimal media containing 1 mM vanillate and protocatechuate, respectively, although wild-type USDA110 was able to grow in both media, indicating that the upregulated copies of vanA1B and pcaG1H1 are exclusively responsible for vanillate degradation. Mutating mxaF eliminated expression of gfa and flhA, which contribute to glutathione-dependent C(1) metabolism. The mxaF mutant had markedly lower cell growth in medium containing vanillate than the wild-type strain. In the presence of protocatechuate, there was no difference in cell growth between the mxaF mutant and the wild-type strain. These results suggest that the C(1) pathway genes are required for efficient vanillate catabolism. In addition, wild-type USDA110 oxidized methanol, whereas the mxaF mutant did not, suggesting that the metabolic capability of the C(1) pathway in B. japonicum extends to methanol oxidation. The mxaF mutant showed normal nodulation and N(2) fixation phenotypes with soybeans, which was not similar to symbiotic phenotypes of methylotrophic rhizobia.
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25
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Itakura M, Saeki K, Omori H, Yokoyama T, Kaneko T, Tabata S, Ohwada T, Tajima S, Uchiumi T, Honnma K, Fujita K, Iwata H, Saeki Y, Hara Y, Ikeda S, Eda S, Mitsui H, Minamisawa K. Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members. THE ISME JOURNAL 2009; 3:326-39. [PMID: 18971963 DOI: 10.1038/ismej.2008.88] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comparative genomic hybridization (CGH) was performed with nine strains of Bradyrhizobium japonicum (a symbiotic nitrogen-fixing bacterium associated with soybean) and eight other members of the Bradyrhizobiaceae by DNA macroarray of B. japonicum USDA110. CGH clearly discriminated genomic variations in B. japonicum strains, but similar CGH patterns were observed in other members of the Bradyrhizobiaceae. The most variable regions were 14 genomic islands (4-97 kb) and low G+C regions on the USDA110 genome, some of which were missing in several strains of B. japonicum and other members of the Bradyrhizobiaceae. The CGH profiles of B. japonicum were classified into three genome types: 110, 122 and 6. Analysis of DNA sequences around the boundary regions showed that at least seven genomic islands were missing in genome type 122 as compared with type 110. Phylogenetic analysis for internal transcribed sequences revealed that strains belonging to genome types 110 and 122 formed separate clades. Thus genomic islands were horizontally inserted into the ancestor genome of type 110 after divergence of the type 110 and 122 strains. To search for functional relationships of variable genomic islands, we conducted linear models of the correlation between the existence of genomic regions and the parameters associated with symbiotic nitrogen fixation in soybean. Variable genomic regions including genomic islands were associated with the enhancement of symbiotic nitrogen fixation in B. japonicum USDA110.
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Affiliation(s)
- Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
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26
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Generation of Bradyrhizobium japonicum mutants with increased N2O reductase activity by selection after introduction of a mutated dnaQ gene. Appl Environ Microbiol 2008; 74:7258-64. [PMID: 18849448 DOI: 10.1128/aem.01850-08] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We obtained two beneficial mutants of Bradyrhizobium japonicum USDA110 with increased nitrous oxide (N(2)O) reductase (N(2)OR) activity by introducing a plasmid containing a mutated B. japonicum dnaQ gene (pKQ2) and performing enrichment culture under selection pressure for N(2)O respiration. Mutation of dnaQ, which encodes the epsilon subunit of DNA polymerase III, gives a strong mutator phenotype in Escherichia coli. pKQ2 introduction into B. japonicum USDA110 increased the frequency of occurrence of colonies spontaneously resistant to kanamycin. A series of repeated cultivations of USDA110 with and without pKQ2 was conducted in anaerobic conditions under 5% (vol/vol) or 20% (vol/vol) N(2)O atmosphere. At the 10th cultivation cycle, cell populations of USDA110(pKQ2) showed higher N(2)OR activity than the wild-type strains. Four bacterial mutants lacking pKQ2 obtained by plant passage showed 7 to 12 times the N(2)OR activity of the wild-type USDA110. Although two mutants had a weak or null fix phenotype for symbiotic nitrogen fixation, the remaining two (5M09 and 5M14) had the same symbiotic nitrogen fixation ability and heterotrophic growth in culture as wild-type USDA110.
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Katsuyama C, Kondo N, Suwa Y, Yamagishi T, Itoh M, Ohte N, Kimura H, Nagaosa K, Kato K. Denitrification Activity and Relevant Bacteria Revealed by Nitrite Reductase Gene Fragments in Soil of Temperate Mixed Forest. Microbes Environ 2008; 23:337-45. [DOI: 10.1264/jsme2.me08541] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chie Katsuyama
- Graducate School of Science and Technology, Shizuoka University
| | - Naho Kondo
- Graduate School of Science, Shizuoka University
| | - Yuichi Suwa
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology
- Department of Biological Sciences, Faculty of Science and Technology, Chuo University
| | - Takao Yamagishi
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology
| | | | - Nobuhito Ohte
- Graduate School of Agriculture, Kyoto University
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Hiroyuki Kimura
- Graduate School of Science, Shizuoka University
- Department of Geosciences, Faculty of Science, Shizuoka University
| | - Kazuyo Nagaosa
- Department of Geosciences, Faculty of Science, Shizuoka University
| | - Kenji Kato
- Graducate School of Science and Technology, Shizuoka University
- Graduate School of Science, Shizuoka University
- Department of Geosciences, Faculty of Science, Shizuoka University
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Ito N, Itakura M, Eda S, Saeki K, Oomori H, Yokoyama T, Kaneko T, Tabata S, Ohwada T, Tajima S, Uchiumi T, Masai E, Tsuda M, Mitsui H, Minamisawa K. Global Gene Expression in Bradyrhizobium japonicum Cultured with Vanillin, Vanillate, 4-Hydroxybenzoate and Protocatechuate. Microbes Environ 2006. [DOI: 10.1264/jsme2.21.240] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Naofumi Ito
- Graduate School of Life Sciences, Tohoku University
| | | | - Shima Eda
- Graduate School of Life Sciences, Tohoku University
| | - Kazuhiko Saeki
- Department of Biological Science, Faculty of Science, Nara Women's University
| | - Hirofumi Oomori
- Department of Biology Graduate School of Science, Osaka University
| | | | | | | | - Takuji Ohwada
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine
| | | | - Toshiki Uchiumi
- Department of Chemistry and BioScience, Faculty of Science, Kagoshima University
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology
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