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Wasai-Hara S, Itakura M, Fernandes Siqueira A, Takemoto D, Sugawara M, Mitsui H, Sato S, Inagaki N, Yamazaki T, Imaizumi-Anraku H, Shimoda Y, Minamisawa K. Bradyrhizobium ottawaense efficiently reduces nitrous oxide through high nosZ gene expression. Sci Rep 2023; 13:18862. [PMID: 37914789 PMCID: PMC10620151 DOI: 10.1038/s41598-023-46019-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
N2O is an important greenhouse gas influencing global warming, and agricultural land is the predominant (anthropogenic) source of N2O emissions. Here, we report the high N2O-reducing activity of Bradyrhizobium ottawaense, suggesting the potential for efficiently mitigating N2O emission from agricultural lands. Among the 15 B. ottawaense isolates examined, the N2O-reducing activities of most (13) strains were approximately five-fold higher than that of Bradyrhizobium diazoefficiens USDA110T under anaerobic conditions. This robust N2O-reducing activity of B. ottawaense was confirmed by N2O reductase (NosZ) protein levels and by mitigation of N2O emitted by nodule decomposition in laboratory system. While the NosZ of B. ottawaense and B. diazoefficiens showed high homology, nosZ gene expression in B. ottawaense was over 150-fold higher than that in B. diazoefficiens USDA110T, suggesting the high N2O-reducing activity of B. ottawaense is achieved by high nos expression. Furthermore, we examined the nos operon transcription start sites and found that, unlike B. diazoefficiens, B. ottawaense has two transcription start sites under N2O-respiring conditions, which may contribute to the high nosZ expression. Our study indicates the potential of B. ottawaense for effective N2O reduction and unique regulation of nos gene expression towards the high performance of N2O mitigation in the soil.
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Affiliation(s)
- Sawa Wasai-Hara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | | | - Daisaku Takemoto
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Masayuki Sugawara
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Noritoshi Inagaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Toshimasa Yamazaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Haruko Imaizumi-Anraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yoshikazu Shimoda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.
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2
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Lyu X, Sun C, Zhang J, Wang C, Zhao S, Ma C, Li S, Li H, Gong Z, Yan C. Integrated Proteomics and Metabolomics Analysis of Nitrogen System Regulation on Soybean Plant Nodulation and Nitrogen Fixation. Int J Mol Sci 2022; 23:2545. [PMID: 35269687 PMCID: PMC8910638 DOI: 10.3390/ijms23052545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/01/2023] Open
Abstract
The specific mechanisms by which nitrogen affects nodulation and nitrogen fixation in leguminous crops are still unclear. To study the relationship between nitrogen, nodulation and nitrogen fixation in soybeans, dual-root soybean plants with unilateral nodulation were prepared by grafting. At the third trifoliate leaf (V3) to fourth trifoliate leaf (V4) growth stages (for 5 days), nitrogen nutrient solution was added to the non-nodulated side, while nitrogen-free nutrient solution was added to the nodulated side. The experiment was designed to study the effects of exogenous nitrogen on proteins and metabolites in root nodules and provide a theoretical reference for analyzing the physiological mechanisms of the interaction between nitrogen application and nitrogen fixation in soybean root nodules. Compared with no nitrogen treatment, exogenous nitrogen regulated the metabolic pathways of starch and sucrose metabolism, organic acid metabolism, nitrogen metabolism, and amino acid metabolism, among others. Additionally, exogenous nitrogen promoted the synthesis of signaling molecules, including putrescine, nitric oxide, and asparagine in root nodules, and inhibited the transformation of sucrose to malic acid; consequently, the rhizobia lacked energy for nitrogen fixation. In addition, exogenous nitrogen reduced cell wall synthesis in the root nodules, thus inhibiting root nodule growth and nitrogen fixation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhenping Gong
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (X.L.); (C.S.); (J.Z.); (C.W.); (S.Z.); (C.M.); (S.L.); (H.L.)
| | - Chao Yan
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (X.L.); (C.S.); (J.Z.); (C.W.); (S.Z.); (C.M.); (S.L.); (H.L.)
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Wendlandt CE, Gano-Cohen KA, Stokes PJN, Jonnala BNR, Zomorrodian AJ, Al-Moussawi K, Sachs JL. Wild legumes maintain beneficial soil rhizobia populations despite decades of nitrogen deposition. Oecologia 2022; 198:419-430. [PMID: 35067801 DOI: 10.1007/s00442-022-05116-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
Abstract
Natural landscapes are increasingly impacted by nitrogen enrichment from aquatic and airborne pollution sources. Nitrogen enrichment in the environment can eliminate the net benefits that plants gain from nitrogen-fixing microbes such as rhizobia, potentially altering host-mediated selection on nitrogen fixation. However, we know little about the long-term effects of nitrogen enrichment on this critical microbial service. Here, we sampled populations of the legume Acmispon strigosus and its associated soil microbial communities from sites spanning an anthropogenic nitrogen deposition gradient. We measured the net growth benefits plants obtained from their local soil microbial communities and quantified plant investment into nodules that house nitrogen-fixing rhizobia. We found that plant growth benefits from sympatric soil microbes did not vary in response to local soil nitrogen levels, and instead varied mainly among plant lines. Soil nitrogen levels positively predicted the number of nodules formed on sympatric plant hosts, although this was likely due to plant genotypic variation in nodule formation, rather than variation among soil microbial communities. The capacity of all the tested soil microbial communities to improve plant growth is consistent with plant populations imposing strong selection on rhizobial nitrogen fixation despite elevated soil nitrogen levels, suggesting that host control traits in A. strigosus are stable under long-term nutrient enrichment.
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Affiliation(s)
- Camille E Wendlandt
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Kelsey A Gano-Cohen
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Peter J N Stokes
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Basava N R Jonnala
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Avissa J Zomorrodian
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Khadija Al-Moussawi
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Joel L Sachs
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA. .,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA. .,Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA.
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4
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Pagano MC, Miransari M, Corrêa EJ, Duarte NF, Yelikbayev BK. Genomic Research Favoring Higher Soybean Production. Curr Genomics 2020; 21:481-490. [PMID: 33214764 PMCID: PMC7604746 DOI: 10.2174/1389202921999200824125710] [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] [Received: 01/15/2020] [Revised: 06/10/2020] [Accepted: 06/19/2020] [Indexed: 11/29/2022] Open
Abstract
Interest in the efficient production of soybean, as one of the most important crop plants, is significantly increasing worldwide. Soybean symbioses, the most important biological process affecting soybean yield and protein content, were revitalized due to the need for sustainable agricultural practices. Similar to many crop species, soybean can establish symbiotic associations with the soil bacteria rhizobia, and with the soil fungi, arbuscular mycorrhizal fungi, and other beneficial rhizospheric microorganisms are often applied as biofertilizers. Microbial interactions may importantly affect soybean production and plant health by activating different genomic pathways in soybean. Genomic research is an important tool, which may be used to elucidate and enhance the mechanisms controlling such actions and interactions. This review presents the available details on the genomic research favoring higher soybean production. Accordingly, new technologies applied to plant rhizosphere and symbiotic microbiota, root-plant endophytes, and details about the genetic composition of soybean inoculant strains are highlighted. Such details may be effectively used to enhance soybean growth and yield, under different conditions, including stress, resulting in a more sustainable production.
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Affiliation(s)
- Marcela C. Pagano
- Address correspondence to these authors at the Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil;, E-mail: and Department of Book&Article, AbtinBerkeh Scienctifc Ltd. Company, Isfahan, Iran; Tel: +98313231755; Fax: +983132504068; E-mail:
| | - Mohammad Miransari
- Address correspondence to these authors at the Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil;, E-mail: and Department of Book&Article, AbtinBerkeh Scienctifc Ltd. Company, Isfahan, Iran; Tel: +98313231755; Fax: +983132504068; E-mail:
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Wang H, Gu C, Liu X, Yang C, Li W, Wang S. Impact of Soybean Nodulation Phenotypes and Nitrogen Fertilizer Levels on the Rhizosphere Bacterial Community. Front Microbiol 2020; 11:750. [PMID: 32528420 PMCID: PMC7247815 DOI: 10.3389/fmicb.2020.00750] [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: 11/29/2019] [Accepted: 03/30/2020] [Indexed: 11/23/2022] Open
Abstract
The effects of nodulation properties of legumes on the rhizosphere bacterial community are still not clear. To determine the effects of nodulation phenotypes on bacterial communities in the rhizosphere of soybean plants, we performed high-throughput sequencing of the 16S rRNA gene to estimate the rhizosphere bacterial community of three soybean lines with different nodulation phenotypes grown in soil supplied with different levels of N fertilizer. The results revealed that both the soybean nodulation phenotypes and the N levels affected the rhizosphere bacteria community, but the nodulation phenotypes contributed more than the N-supply. The diversity of bacteria was decreased in the rhizosphere of super-nodulating phenotype. The response of rhizosphere bacterial communities to the soil available nitrogen (AN) concentrations was different than the response with the three nodulation phenotypes of soybean which was more stable in the wild-type (Nod+) soybean samples than that in the mutant samples (Nod– and Nod++). Bradyrhizobium in the rhizosphere was positively correlated with nodule number and negatively correlated to AN in the soil, while Burkholderia and Dyella were positively correlated with nodule biomass and nitrogenase activity. These results demonstrated that the nodulation phenotype of soybean affects the rhizosphere microbiome.
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Affiliation(s)
- Hao Wang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Chuntao Gu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Xiaofeng Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Chunwei Yang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Shaodong Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
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Sun X, Liu H, Wang P, Wang L, Ni W, Yang Q, Wang H, Tang H, Zhao G, Zheng Z. Construction of a novel MK-4 biosynthetic pathway in Pichia pastoris through heterologous expression of HsUBIAD1. Microb Cell Fact 2019; 18:169. [PMID: 31601211 PMCID: PMC6786277 DOI: 10.1186/s12934-019-1215-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Background With a variety of physiological and pharmacological functions, menaquinone is an essential prenylated product that can be endogenously converted from phylloquinone (VK1) or menadione (VK3) via the expression of Homo sapiens UBIAD1 (HsUBIAD1). The methylotrophic yeast, Pichia pastoris, is an attractive expression system that has been successfully applied to the efficient expression of heterologous proteins. However, the menaquinone biosynthetic pathway has not been discovered in P. pastoris. Results Firstly, we constructed a novel synthetic pathway in P. pastoris for the production of menaquinone-4 (MK-4) via heterologous expression of HsUBIAD1. Then, the glyceraldehyde-3-phosphate dehydrogenase constitutive promoter (PGAP) appeared to be mostsuitable for the expression of HsUBIAD1 for various reasons. By optimizing the expression conditions of HsUBIAD1, its yield increased by 4.37 times after incubation at pH 7.0 and 24 °C for 36 h, when compared with that under the initial conditions. We found HsUBIAD1 expressed in recombinant GGU-23 has the ability to catalyze the biosynthesis of MK-4 when using VK1 and VK3 as the isopentenyl acceptor. In addition, we constructed a ribosomal DNA (rDNA)-mediated multi-copy expression vector for the fusion expression of SaGGPPS and PpIDI, and the recombinant GGU-GrIG afforded higher MK-4 production, so that it was selected as the high-yield strain. Finally, the yield of MK-4 was maximized at 0.24 mg/g DCW by improving the GGPP supply when VK3 was the isopentenyl acceptor. Conclusions In this study, we constructed a novel synthetic pathway in P. pastoris for the biosynthesis of the high value-added prenylated product MK-4 through heterologous expression of HsUBIAD1 and strengthened accumulation of GGPP. This approach could be further developed and accomplished for the biosynthesis of other prenylated products, which has great significance for theoretical research and industrial application.
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Affiliation(s)
- Xiaowen Sun
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Hui Liu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Peng Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Li Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Wenfeng Ni
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Qiang Yang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Han Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Hengfang Tang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Genhai Zhao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.
| | - Zhiming Zheng
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.
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