1
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Alon M, Waitz Y, Finkel OM, Sheffer E. The native distribution of a common legume shrub is limited by the range of its nitrogen-fixing mutualist. New Phytol 2024; 242:77-92. [PMID: 38339826 DOI: 10.1111/nph.19577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 01/20/2024] [Indexed: 02/12/2024]
Abstract
Plant-microbe mutualisms, such as the legume-rhizobium symbiosis, are influenced by the geographical distributions of both partners. However, limitations on the native range of legumes, resulting from the absence of a compatible mutualist, have rarely been explored. We used a combination of a large-scale field survey and controlled experiments to determine the realized niche of Calicotome villosa, an abundant and widespread legume shrub. Soil type was a major factor affecting the distribution and abundance of C. villosa. In addition, we found a large region within its range in which neither C. villosa nor Bradyrhizobium, the bacterial genus that associates with it, were present. Seedlings grown in soil from this region failed to nodulate and were deficient in nitrogen. Inoculation of this soil with Bradyrhizobium isolated from root nodules of C. villosa resulted in the formation of nodules and higher growth rate, leaf N and shoot biomass compared with un-inoculated plants. We present evidence for the exclusion of a legume from parts of its native range by the absence of a compatible mutualist. This result highlights the importance of the co-distribution of both the host plant and its mutualist when attempting to understand present and future geographical distributions of legumes.
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Affiliation(s)
- Moshe Alon
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Yoni Waitz
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Omri M Finkel
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Efrat Sheffer
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
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2
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Dong X, Shi X, Cui Z, Dai W, Dong F. Dynamic Hydroxylation Enhances Hydrogen Atom Abstraction from Water for Nitrogen Fixation Revealed by Isotope Labeling in Situ Fourier-Transform Infrared Spectroscopy. ACS Nano 2024. [PMID: 38516986 DOI: 10.1021/acsnano.4c00975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Employing water as a hydrogen source to participate in the hydrogen atom transfer (HAT) process is a low-cost and carbon-free process demonstrating great economic and environmental potential in catalysis. However, the low efficiency of hydrogen atom abstraction from water leads to slow kinetics of HAT for most hydrogenative reactions. Here, we prepared ultrathin Bi4O5Cl2 nanosheets where the surface can be in situ reconstructed via hydroxylation under light illumination to facilitate the abstraction of hydrogen atoms from pure water for efficient nitrogen fixation. Consequently, the isotope labeling in situ Fourier-transform infrared spectroscopy (FT-IR) involving H2O and D2O has clearly revealed that the hydroxyl groups tend to be adsorbed on the chloride vacancy sites on the Bi4O5Cl2 surface to form hydroxylated surfaces, where the hydroxylated photocatalyst surface enables partial dehydrogenation of water into H2O2, allowing the utilization of H atoms for efficient of N2 hydrogenation via HAT steps. This work elucidates the in-depth reaction mechanism of hydrogen atom extraction from H2O molecules via the light-generated chloride vacancy to promote photocatalytic nitrogen fixation, ultimately enabling the inspiration and providing crucial rules for the design of important functional materials that can efficiently deliver active hydrogen for chemical synthesis.
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Affiliation(s)
- Xing'an Dong
- Research Center for Carbon-Neutral Environmental & Energy Technology, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, People's Republic of China
- College of Physics and Electronic Engineering, Chongqing Normal University, Chongqing 401331, People's Republic of China
| | - Xian Shi
- School of Chemistry and Environmental Engineering, Sichuan University of Science & Engineering, Zigong 643000, People's Republic of China
| | - Zhihao Cui
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Weidong Dai
- Research Center for Carbon-Neutral Environmental & Energy Technology, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, People's Republic of China
| | - Fan Dong
- Research Center for Carbon-Neutral Environmental & Energy Technology, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, People's Republic of China
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Qu Z, Zhou R, Sun J, Gao Y, Li Z, Zhang T, Zhou R, Liu D, Tu X, Cullen P, Ostrikov KK. Plasma-Assisted Sustainable Nitrogen-to-Ammonia Fixation: Mixed-phase, Synergistic Processes and Mechanisms. ChemSusChem 2024; 17:e202300783. [PMID: 37994281 DOI: 10.1002/cssc.202300783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 11/24/2023]
Abstract
Ammonia plays a crucial role in industry and agriculture worldwide, but traditional industrial ammonia production methods are energy-intensive and negatively impact the environment. Ammonia synthesis using low-temperature plasma technology has gained traction in the pursuit of environment-benign and cost-effective methods for producing green ammonia. This Review discusses the recent advances in low-temperature plasma-assisted ammonia synthesis, focusing on three main routes: N2+H2 plasma-only, N2+H2O plasma-only, and plasma coupled with other technologies. The reaction pathways involved in the plasma-assisted ammonia synthesis, as well as the process parameters, including the optimum catalyst types and discharge schemes, are examined. Building upon the current research status, the challenges and research opportunities in the plasma-assisted ammonia synthesis processes are outlined. The article concludes with the outlook for the future development of the plasma-assisted ammonia synthesis technology in real-life industrial applications.
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Affiliation(s)
- Zhongping Qu
- State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi An Shi, Xi'an, 710049, P. R. China
| | - Renwu Zhou
- State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi An Shi, Xi'an, 710049, P. R. China
| | - Jing Sun
- State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi An Shi, Xi'an, 710049, P. R. China
| | - Yuting Gao
- State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi An Shi, Xi'an, 710049, P. R. China
| | - Zhuo Li
- State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi An Shi, Xi'an, 710049, P. R. China
| | - Tianqi Zhang
- School of Chemical and Biomolecular Engineering, University of Sydney, New South Wales, Darlington, 2008, Australia
| | - Rusen Zhou
- School of Chemical and Biomolecular Engineering, University of Sydney, New South Wales, Darlington, 2008, Australia
| | - Dingxin Liu
- State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi An Shi, Xi'an, 710049, P. R. China
| | - Xin Tu
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, L69 3GJ, United Kingdom
| | - Patrick Cullen
- School of Chemical and Biomolecular Engineering, University of Sydney, New South Wales, Darlington, 2008, Australia
| | - Kostya Ken Ostrikov
- School of Chemistry and Physics and Centre for Materials Science, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
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Lam M, Leung KM, Lai GKK, Leung FCC, Griffin SDJ. Complete genome sequence of Klebsiella variicola subsp. variicola ML.9ba2, an endophytic strain isolated from aerial roots of Philodendron erubescens. Microbiol Resour Announc 2024:e0116323. [PMID: 38509053 DOI: 10.1128/mra.01163-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/02/2024] [Indexed: 03/22/2024] Open
Abstract
The endophytic strain Klebsiella variicola subsp. variicola ML.9ba2 was isolated from aerial roots of Philodendron erubescens in Hong Kong. Its complete genome of 5,682,083 bp (57.29% G+C), comprising a single chromosome and an IncF plasmid, was established through hybrid assembly.
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Affiliation(s)
- M Lam
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - K M Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - G K K Lai
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - F C C Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - S D J Griffin
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
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Russell SJ, Garcia AK, Kaçar B. A CRISPR interference system for engineering biological nitrogen fixation. mSystems 2024; 9:e0015524. [PMID: 38376168 PMCID: PMC10949490 DOI: 10.1128/msystems.00155-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
A grand challenge for the next century is in facing a changing climate through bioengineering solutions. Biological nitrogen fixation, the globally consequential, nitrogenase-catalyzed reduction of atmospheric nitrogen to bioavailable ammonia, is a vital area of focus. Nitrogen fixation engineering relies upon extensive understanding of underlying genetics in microbial models, including the broadly utilized gammaproteobacterium, Azotobacter vinelandii (A. vinelandii). Here, we report the first CRISPR interference (CRISPRi) system for targeted gene silencing in A. vinelandii that integrates genomically via site-specific transposon insertion. We demonstrate that CRISPRi can repress transcription of an essential nitrogen fixation gene by ~60%. Further, we show that nitrogenase genes are suitably expressed from the transposon insertion site, indicating that CRISPRi and engineered nitrogen fixation genes can be co-integrated for combinatorial studies of gene expression and engineering. Our established CRISPRi system fills an important gap for engineering microbial nitrogen fixation for desired purposes.IMPORTANCEAll life on Earth requires nitrogen to survive. About 78% of the atmosphere alone is nitrogen, yet humans cannot use it directly. Instead, we obtain the nitrogen we need for our survival through the food we eat. For more than 100 years, a substantial portion of agricultural productivity has relied on industrial methods for nitrogen fertilizer synthesis, which consumes significant amounts of nonrenewable energy resources and exacerbates environmental degradation and human-induced climate change. Promising alternatives to these industrial methods rely on engineering the only biological pathway for generating bioaccessible nitrogen: microbial nitrogen fixation. Bioengineering strategies require an extensive understanding of underlying genetics in nitrogen-fixing microbes, but genetic tools for this critical goal remain lacking. The CRISPRi gene silencing system that we report, developed in the broadly utilized nitrogen-fixing bacterial model, Azotobacter vinelandii, is an important step toward elucidating the complexity of nitrogen fixation genetics and enabling their manipulation.
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Affiliation(s)
- Steven J. Russell
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amanda K. Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Addison H, Glatter T, K. A. Hochberg G, Rebelein JG. Two distinct ferredoxins are essential for nitrogen fixation by the iron nitrogenase in Rhodobacter capsulatus. mBio 2024; 15:e0331423. [PMID: 38377621 PMCID: PMC10936413 DOI: 10.1128/mbio.03314-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Nitrogenases are the only enzymes able to fix gaseous nitrogen into bioavailable ammonia and hence are essential for sustaining life. Catalysis by nitrogenases requires both a large amount of ATP and electrons donated by strongly reducing ferredoxins or flavodoxins. Our knowledge about the mechanisms of electron transfer to nitrogenase enzymes is limited: The electron transport to the iron (Fe)-nitrogenase has hardly been investigated. Here, we characterized the electron transfer pathway to the Fe-nitrogenase in Rhodobacter capsulatus via proteome analyses, genetic deletions, complementation studies, and phylogenetics. Proteome analyses revealed an upregulation of four ferredoxins under nitrogen-fixing conditions reliant on the Fe-nitrogenase in a molybdenum nitrogenase knockout strain, compared to non-nitrogen-fixing conditions. Based on these findings, R. capsulatus strains with deletions of ferredoxin (fdx) and flavodoxin (fld, nifF) genes were constructed to investigate their roles in nitrogen fixation by the Fe-nitrogenase. R. capsulatus deletion strains were characterized by monitoring diazotrophic growth and Fe-nitrogenase activity in vivo. Only deletions of fdxC or fdxN resulted in slower growth and reduced Fe-nitrogenase activity, whereas the double deletion of both fdxC and fdxN abolished diazotrophic growth. Differences in the proteomes of ∆fdxC and ∆fdxN strains, in conjunction with differing plasmid complementation behaviors of fdxC and fdxN, indicate that the two Fds likely possess different roles and functions. These findings will guide future engineering of the electron transport systems to nitrogenase enzymes, with the aim of increased electron flux and product formation.IMPORTANCENitrogenases are essential for biological nitrogen fixation, converting atmospheric nitrogen gas to bioavailable ammonia. The production of ammonia by diazotrophic organisms, harboring nitrogenases, is essential for sustaining plant growth. Hence, there is a large scientific interest in understanding the cellular mechanisms for nitrogen fixation via nitrogenases. Nitrogenases rely on highly reduced electrons to power catalysis, although we lack knowledge as to which proteins shuttle the electrons to nitrogenases within cells. Here, we characterized the electron transport to the iron (Fe)-nitrogenase in the model diazotroph Rhodobacter capsulatus, showing that two distinct ferredoxins are very important for nitrogen fixation despite having different redox centers. In addition, our research expands upon the debate on whether ferredoxins have functional redundancy or perform distinct roles within cells. Here, we observe that both essential ferredoxins likely have distinct roles based on differential proteome shifts of deletion strains and different complementation behaviors.
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Affiliation(s)
- Holly Addison
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg K. A. Hochberg
- Evolutionary Biochemistry Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Johannes G. Rebelein
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
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7
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Sinharoy S, Tian CF, Montiel J. Editorial: Plant-rhizobia symbiosis and nitrogen fixation in legumes. Front Plant Sci 2024; 15:1392006. [PMID: 38529060 PMCID: PMC10961434 DOI: 10.3389/fpls.2024.1392006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/27/2024]
Affiliation(s)
- Senjuti Sinharoy
- Plant-Microbe Interaction, National Institute of Plant Genome Research (NIPGR) New Delhi, New Delhi, India
| | - Chang-Fu Tian
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jesús Montiel
- Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
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Pan H, Shim A, Lubin MB, Belin BJ. Hopanoid lipids promote soybean -Bradyrhizobium symbiosis. mBio 2024:e0247823. [PMID: 38445860 DOI: 10.1128/mbio.02478-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/04/2024] [Indexed: 03/07/2024] Open
Abstract
The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote Bradyrhizobium symbioses with tropical legumes. To characterize hopanoids in Bradyrhizobium symbiosis with soybean, we validated a recently published cumate-inducible hopanoid mutant of Bradyrhizobium diazoefficiens USDA110, Pcu-shc::∆shc. GC-MS analysis showed that this strain does not produce hopanoids without cumate induction, and under this condition, is impaired in growth in rich medium and under osmotic, temperature, and pH stress. In planta, Pcu-shc::∆shc is an inefficient soybean symbiont with significantly lower rates of nitrogen fixation and low survival within the host tissue. RNA-seq revealed that hopanoid loss reduces the expression of flagellar motility and chemotaxis-related genes, further confirmed by swim plate assays, and enhances the expression of genes related to nitrogen metabolism and protein secretion. These results suggest that hopanoids provide a significant fitness advantage to B. diazoefficiens in legume hosts and provide a foundation for future mechanistic studies of hopanoid function in protein secretion and motility. A major problem for global sustainability is feeding our exponentially growing human population while available arable land decreases. Harnessing the power of plant-beneficial microbes is a potential solution, including increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis between Bradyrhizobium diazoefficiens USDA110, an important commercial inoculant strain, and its economically significant host soybean. Our research extends our knowledge of the functions of bacterial lipids in symbiosis to an agricultural context, which may one day help improve the practical applications of plant-beneficial microbes in agriculture.
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Affiliation(s)
- Huiqiao Pan
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, USA
| | - Ashley Shim
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Matthew B Lubin
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Brittany J Belin
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
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Peng C, Zhang X, Li J, Yang M, Ma S, Fan H, Dai L, Cheng L. Oleispirillum naphthae gen. nov., sp. nov., a bacterium isolated from oil sludge, and proposal of Oleispirillaceae fam. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38512751 DOI: 10.1099/ijsem.0.006292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024] Open
Abstract
A microaerophilic, Gram-negative, motile, and spiral-shaped bacterium, designated Y-M2T, was isolated from oil sludge of Shengli oil field. The optimal growth condition of strain Y-M2T was at 25 °C, pH 7.0, and in the absence of NaCl. The major polar lipid was phosphatidylethanolamine. The main cellular fatty acid was iso-C17 : 0 3-OH. It contained Q-9 and Q-10 as the predominant quinones. The DNA G+C content was 68.1 mol%. Strain Y-M2T showed the highest 16S rRNA gene sequence similarity to Telmatospirillum siberiense 26-4bT (91.1 %). Phylogenetic analyses based on 16S rRNA gene and genomes showed that strain Y-M2T formed a distinct cluster in the order Rhodospirillales. Genomic analysis showed that Y-M2T possesses a complete nitrogen-fixation cluster which is phylogenetically close to that of methanogene. The nif cluster, encompassing the nitrogenase genes, was found in every N2-fixing strain within the order Rhodospirillales. Phylogeny, phenotype, chemotaxonomy, and genomic results demonstrated that strain Y-M2T represents a novel species of a novel genus in a novel family Oleispirillaceae fam. nov. in the order Rhodospirillales, for which the name Oleispirillum naphthae gen. nov., sp. nov. was proposed. The type strain is Y-M2T (=CCAM 827T=JCM 34765T).
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Affiliation(s)
- Chenghui Peng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Xue Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Shichun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu 610213, Sichuan Province, PR China
| | - Hui Fan
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Lirong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu 610213, Sichuan Province, PR China
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Liu N, Kivenson V, Peng X, Cui Z, Lankiewicz TS, Gosselin KM, English CJ, Blair EM, O'Malley MA, Valentine DL. Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen. Appl Environ Microbiol 2024; 90:e0091423. [PMID: 38265213 PMCID: PMC10880615 DOI: 10.1128/aem.00914-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024] Open
Abstract
Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.
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Affiliation(s)
- Na Liu
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Veronika Kivenson
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Xuefeng Peng
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, China
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Kelsey M. Gosselin
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Chance J. English
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Ecology Evolution, and Marine Biology, University of California, Santa Barbara, California, USA
| | - Elaina M. Blair
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
- Biological Engineering Program, University of California, Santa Barbara, California, USA
| | - David L. Valentine
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Earth Science, University of California Santa Barbara, Santa Barbara, California, USA
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Han F, Li H, Lyu E, Zhang Q, Gai H, Xu Y, Bai X, He X, Khan AQ, Li X, Xie F, Li F, Fang X, Wei M. Soybean-mediated suppression of BjaI/BjaR 1 quorum sensing in Bradyrhizobium diazoefficiens impacts symbiotic nitrogen fixation. Appl Environ Microbiol 2024; 90:e0137423. [PMID: 38251894 PMCID: PMC10880635 DOI: 10.1128/aem.01374-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024] Open
Abstract
The acyl-homoserine lactones (AHLs)-mediated LuxI/LuxR quorum sensing (QS) system orchestrates diverse bacterial behaviors in response to changes in population density. The role of the BjaI/BjaR1 QS system in Bradyrhizobium diazoefficiens USDA 110, which shares homology with LuxI/LuxR, remains elusive during symbiotic interaction with soybean. Here this genetic system in wild-type (WT) bacteria residing inside nodules exhibited significantly reduced activity compared to free-living cells, potentially attributed to soybean-mediated suppression. The deletion mutant strain ΔbjaR1 showed significantly enhanced nodulation induction and nitrogen fixation ability. Nevertheless, its ultimate symbiotic outcome (plant dry weight) in soybeans was compromised. Furthermore, comparative analysis of the transcriptome, proteome, and promoter activity revealed that the inactivation of BjaR1 systematically activated and inhibited genomic modules associated with nodulation and nitrogen metabolism. The former appeared to be linked to a significant decrease in the expression of NodD2, a key cell-density-dependent repressor of nodulation genes, while the latter conferred bacterial growth and nitrogen fixation insensitivity to environmental nitrogen. In addition, BjaR1 exerted a positive influence on the transcription of multiple genes involved in a so-called central intermediate metabolism within the nodule. In conclusion, our findings highlight the crucial role of the BjaI/BjaR1 QS circuit in positively regulating bacterial nitrogen metabolism and emphasize the significance of the soybean-mediated suppression of this genetic system for promoting efficient symbiotic nitrogen fixation by B. diazoefficiens.IMPORTANCEThe present study demonstrates, for the first time, that the BjaI/BjaR1 QS system of Bradyrhizobium diazoefficiens has a significant impact on its nodulation and nitrogen fixation capability in soybean by positively regulating NodD2 expression and bacterial nitrogen metabolism. Moreover, it provides novel insights into the importance of suppressing the activity of this QS circuit by the soybean host plant in establishing an efficient mutual relationship between the two symbiotic partners. This research expands our understanding of legumes' role in modulating symbiotic nitrogen fixation through rhizobial QS-mediated metabolic functioning, thereby deepening our comprehension of symbiotic coevolution theory. In addition, these findings may hold great promise for developing quorum quenching technology in agriculture.
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Affiliation(s)
- Fang Han
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Huiquan Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ermeng Lyu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qianqian Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Haoyu Gai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yunfang Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xuemei Bai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xueqian He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Abdul Qadir Khan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaolin Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Fengmin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiangwen Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Min Wei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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12
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Miller V, Clark DS, Mesbah A. Ammonia Retention in Biowaste via Low-Temperature-Plasma-Synthesized Nitrogen Oxyacids: Toward Sustainable Upcycling of Animal Waste. ACS Sustain Chem Eng 2024; 12:2621-2631. [PMID: 38389902 PMCID: PMC10880101 DOI: 10.1021/acssuschemeng.3c06423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/24/2024]
Abstract
Sustainable fertilizer production is a pressing challenge due to a growing human population. The manufacture of synthetic nitrogen fertilizer involves intensive emissions of greenhouse gases. The synthetic nitrogen that ends up in biowaste such as animal waste perturbs the nitrogen cycle through significant nitrogen losses in the form of ammonia volatilization, a major human health and environmental hazard. Low-temperature air-plasma treatment of animal waste holds promise for sustainable fertilizer production on farmlands by enabling nitrogen fixation via ionization, forming nitrogen oxyacids. Although the formation of nitrogen oxyacids in plasma treatment of water is well-established, the extent of nitrogen oxyanion enrichment in animal waste and its downstream effects on acidifying the waste remain elusive because many compounds found in complex biowaste media may interfere with absorbed NOx species. This work aims to establish that plasma treatment of dairy manure can suppress ammonia loss by volatilization via acidification of animal waste while enriching the waste in total nitrogen due to nitrogen retained in ammonia as well as adding nitrogen oxyacids by reacting NOx with the aqueous slurry. To this end, air-plasma effluent containing NOx is bubbled through dairy manure, which is then analyzed for changes in the nitrogen oxyanion content and pH. Increasing the plasma treatment time results in more acidic manure, reduced ammonium content in the downstream acid trap, and increased nitrogen oxyanion content, where the yield of nitrogen oxyanion from absorbed NOx species is approximately 100%. Increased plasma treatment also led to an increase in the total Kjeldahl nitrogen and the total nitrogen. These results indicate that plasma treatment of animal waste can significantly suppress ammonia pollution from animal husbandry facilities such as dairy farms while upcycling animal waste as a rich organic source of nitrogen.
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Affiliation(s)
- Victor
V. Miller
- Department of Chemical and
Biomolecular Engineering, University of
California, Berkeley, California 94720, United States
| | - Douglas S. Clark
- Department of Chemical and
Biomolecular Engineering, University of
California, Berkeley, California 94720, United States
| | - Ali Mesbah
- Department of Chemical and
Biomolecular Engineering, University of
California, Berkeley, California 94720, United States
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13
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Dobrzyńska K, Pérez-González A, Echavarri-Erasun C, Coroian D, Salinero-Lanzarote A, Veldhuizen M, Dean DR, Burén S, Rubio LM. Nitrogenase cofactor biosynthesis using proteins produced in mitochondria of Saccharomyces cerevisiae. mBio 2024; 15:e0308823. [PMID: 38126768 PMCID: PMC10865832 DOI: 10.1128/mbio.03088-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Biological nitrogen fixation, the conversion of inert N2 to metabolically tractable NH3, is only performed by certain microorganisms called diazotrophs and is catalyzed by the nitrogenases. A [7Fe-9S-C-Mo-R-homocitrate]-cofactor, designated FeMo-co, provides the catalytic site for N2 reduction in the Mo-dependent nitrogenase. Thus, achieving FeMo-co formation in model eukaryotic organisms, such as Saccharomyces cerevisiae, represents an important milestone toward endowing them with a capacity for Mo-dependent biological nitrogen fixation. A central player in FeMo-co assembly is the scaffold protein NifEN upon which processing of NifB-co, an [8Fe-9S-C] precursor produced by NifB, occurs. Prior work established that NifB-co can be produced in S. cerevisiae mitochondria. In the present work, a library of nifEN genes from diverse diazotrophs was expressed in S. cerevisiae, targeted to mitochondria, and surveyed for their ability to produce soluble NifEN protein complexes. Many such NifEN variants supported FeMo-co formation when heterologously produced in the diazotroph A. vinelandii. However, only three of them accumulated in soluble forms in mitochondria of aerobically cultured S. cerevisiae. Of these, two variants were active in the in vitro FeMo-co synthesis assay. NifEN, NifB, and NifH proteins from different species, all of them produced in and purified from S. cerevisiae mitochondria, were combined to establish successful FeMo-co biosynthetic pathways. These findings demonstrate that combining diverse interspecies nitrogenase FeMo-co assembly components could be an effective and, perhaps, the only approach to achieve and optimize nitrogen fixation in a eukaryotic organism.IMPORTANCEBiological nitrogen fixation, the conversion of inert N2 to metabolically usable NH3, is a process exclusive to diazotrophic microorganisms and relies on the activity of nitrogenases. The assembly of the nitrogenase [7Fe-9S-C-Mo-R-homocitrate]-cofactor (FeMo-co) in a eukaryotic cell is a pivotal milestone that will pave the way to engineer cereals with nitrogen fixing capabilities and therefore independent of nitrogen fertilizers. In this study, we identified NifEN protein complexes that were functional in the model eukaryotic organism Saccharomyces cerevisiae. NifEN is an essential component of the FeMo-co biosynthesis pathway. Furthermore, the FeMo-co biosynthetic pathway was recapitulated in vitro using only proteins expressed in S. cerevisiae. FeMo-co biosynthesis was achieved by combining nitrogenase FeMo-co assembly components from different species, a promising strategy to engineer nitrogen fixation in eukaryotic organisms.
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Affiliation(s)
- Katarzyna Dobrzyńska
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Diana Coroian
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Alvaro Salinero-Lanzarote
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Marcel Veldhuizen
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Dennis R. Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Luis M. Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
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14
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Yuan J, Feng W, Zhang Y, Xiao J, Zhang X, Wu Y, Ni W, Huang H, Dai W. Unraveling Synergistic Effect of Defects and Piezoelectric Field in Breakthrough Piezo-Photocatalytic N 2 Reduction. Adv Mater 2024; 36:e2303845. [PMID: 37638643 DOI: 10.1002/adma.202303845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/27/2023] [Indexed: 08/29/2023]
Abstract
Piezo-photocatalysis is a frontier technology for converting mechanical and solar energies into crucial chemical substances and has emerged as a promising and sustainable strategy for N2 fixation. Here, for the first time, defects and piezoelectric field are synergized to achieve unprecedented piezo-photocatalytic nitrogen reduction reaction (NRR) activity and their collaborative catalytic mechanism is unraveled over BaTiO3 with tunable oxygen vacancies (OVs). The introduced OVs change the local dipole state to strengthen the piezoelectric polarization of BaTiO3 , resulting in a more efficient separation of photogenerated carrier. Ti3+ sites adjacent to OVs promote N2 chemisorption and activation through d-π back-donation with the help of the unpaired d-orbital electron. Furthermore, a piezoelectric polarization field could modulate the electronic structure of Ti3+ to facilitate the activation and dissociation of N2 , thereby substantially reducing the reaction barrier of the rate-limiting step. Benefitting from the synergistic reinforcement mechanism and optimized surface dynamics processes, an exceptional piezo-photocatalytic NH3 evolution rate of 106.7 µmol g-1 h-1 is delivered by BaTiO3 with moderate OVs, far surpassing that of previously reported piezocatalysts/piezo-photocatalysts. New perspectives are provided here for the rational design of an efficient piezo-photocatalytic system for the NRR.
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Affiliation(s)
- Jie Yuan
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Wenhui Feng
- Hunan Province Key Laboratory of Applied Environmental Photocatalysis, Changsha University, Changsha, 410022, P. R. China
| | - Yongfan Zhang
- College of Chemistry, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Jianyu Xiao
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Xiaoyan Zhang
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Yinting Wu
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Wenkang Ni
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, 350116, P. R. China
| | - Hongwei Huang
- Beijing Key Laboratory of Materials Utilization of Nonmetallic Minerals and Solid Wastes, National Laboratory of Mineral Materials, School of Materials Science and Technology, China University of Geosciences, Beijing, 100083, P. R. China
| | - Wenxin Dai
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, 350116, P. R. China
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15
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Li Y, Liu Q, Zhang DX, Zhang ZY, Xu A, Jiang YL, Chen ZC. Metal nutrition and transport in the process of symbiotic nitrogen fixation. Plant Commun 2024:100829. [PMID: 38303509 DOI: 10.1016/j.xplc.2024.100829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/14/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
Symbiotic nitrogen fixation (SNF) facilitated by the interaction between legumes and rhizobia is a well-documented and eco-friendly alternative to chemical nitrogen fertilizers. Host plants obtain fixed nitrogen from rhizobia by providing carbon and mineral nutrients. These mineral nutrients, which are mostly in the form of metal ions, are implicated in various stages of the SNF process. This review describes the functional roles played by metal ions in nodule formation and nitrogen fixation and specifically addresses their transport mechanisms and associated transporters within root nodules. Future research directions and potential strategies for enhancing SNF efficiency are also discussed.
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Affiliation(s)
- Yuan Li
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qian Liu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dan-Xun Zhang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhuo-Yan Zhang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ao Xu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Long Jiang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhi-Chang Chen
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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16
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Liu P, Liu Y, Zhang A, Liu Z, Yang L, Yang Z. Catalytic Ozonation of Air toward Direct Nitric Acid Production Using Hierarchical Co 3O 4 with a Tunable Microstructure. ACS Appl Mater Interfaces 2024; 16:3564-3575. [PMID: 38206319 DOI: 10.1021/acsami.3c17649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The nitrogen oxidation reaction (NOR) to form nitric acid by applying natural air and H2O under ambient conditions is a sustainable approach to achieving efficient and selective N2 fixation for industrial applications. In this study, four kinds of Co3O4 catalysts with a controllable microstructure were prepared to catalyze the direct NOR of N2 in the air. At the same time, the reaction mechanism of the conversion of N2 to nitric acid under catalytic ozonation was explored through experimental research and density functional theory (DFT) calculation. The results showed that the prepared porous nanosheets self-assembled into microflower-structured samples. The HCOF showed extraordinary catalytic performance for direct NOR to produce a high concentration of nitric acid. The maximum rate of nitric acid formation could be as high as 6.67 mmol/(h·gcat), which was higher than those of most reported photocatalytic or electrocatalytic N2 fixation processes for direct NOR to produce NO3-. Furthermore, the 15N isotopic-labeling experiment confirmed that the produced NO3- originated from N2 in the air by the direct NOR process. In the direct NOR mechanism, inert N2 molecules were captured at the Co3+ active sites by the acceptance-donation electron conduction mode, and the oxygen vacancies boosted the chemical adsorption of N2 molecules and greatly reduced the activation energy barrier of N2 molecules. The active free radicals •OH and •O2- generated by the decomposition of O3 molecules oxidized N2 to the intermediate *NO, which was the rate-determining step, and it was then absorbed by water to form nitric acid. The air catalytic ozonation method in this study was proposed as a facile pathway for efficient nitrogen fixation. This research provides a new method for environmental protection and efficient production of nitric acid at distributed sources.
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Affiliation(s)
- Pan Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, P. R. China
- Xi'an Aeronautical Polytechnic Institute, Xi'an 710089, P. R. China
| | - Yongjun Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, P. R. China
| | - Aining Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, P. R. China
| | - Zhe Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, P. R. China
| | - Lu Yang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, P. R. China
| | - Zhuangzhuang Yang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, P. R. China
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17
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Zhang S, Chen D, Chen P, Zhang R, Hou Y, Guo Y, Li P, Liang X, Xing T, Chen J, Zhao Y, Huang Z, Lei D, Zhi C. Concurrent Mechanisms of Hot Electrons and Interfacial Water Molecule Ordering in Plasmon-Enhanced Nitrogen Fixation. Adv Mater 2024:e2310776. [PMID: 38234149 DOI: 10.1002/adma.202310776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/08/2024] [Indexed: 01/19/2024]
Abstract
The participation of high-energy hot electrons generated from the non-radiative decay of localized surface plasmons is an important mechanism for promoting catalytic processes. Herein, another vital mechanism associated with the localized surface plasmon resonance (LSPR) effect, significantly contributing to the nitrogen reduction reaction (NRR), is found. That is to say, the LSPR-induced strong localized electric fields can weaken the intermolecular hydrogen bonds and regulate the arrangement of water molecules at the solid-liquid interface. The AuCu pentacle nanoparticles with excellent light absorption ability and the capability to generate strong localized electric fields are chosen to demonstrate this effect. The in situ Raman spectra and theoretical calculations are employed to verify the mechanism at the molecular scale in a nitrogen fixation process. Meanwhile, due to the promoted electron transfer at the interface by the well-ordered interfacial water, as well as the participation of high-energy hot electrons, the optimal catalyst exhibits excellent performance with an NH3 yield of 52.09 µg h-1 cm-2 and Faradaic efficiency (FE) of 45.82% at ─0.20 V versus RHE. The results are significant for understanding the LSPR effect in catalysis and provide a new approach for regulating the reaction process.
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Affiliation(s)
- Shaoce Zhang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Dong Chen
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Peigang Chen
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Rong Zhang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Yue Hou
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Ying Guo
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Pei Li
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Xiu Liang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Tingyang Xing
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Jie Chen
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Yuwei Zhao
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Zhaodong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- Centre for Functional Photonics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Dangyuan Lei
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- Centre for Functional Photonics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
- Hong Kong Branch of National Precious Metals Material Engineering Research Centre, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, 999077, China
| | - Chunyi Zhi
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- Centre for Functional Photonics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
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18
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Dietz BR, Olszewski NE, Barney BM. Enhanced extracellular ammonium release in the plant endophyte Gluconacetobacter diazotrophicus through genome editing. Microbiol Spectr 2024; 12:e0247823. [PMID: 38038458 PMCID: PMC10783055 DOI: 10.1128/spectrum.02478-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE Our results demonstrate increased extracellular ammonium release in the endophyte plant growth-promoting bacterium Gluconacetobacter diazotrophicus. Strains were constructed in a manner that leaves no antibiotic markers behind, such that these strains contain no transgenes. Levels of ammonium achieved by cultures of modified G. diazotrophicus strains reached concentrations of approximately 18 mM ammonium, while wild-type G. diazotrophicus remained much lower (below 50 µM). These findings demonstrate a strong potential for further improving the biofertilizer potential of this important microbe.
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Affiliation(s)
- Benjamin R. Dietz
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA
| | - Neil E. Olszewski
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Brett M. Barney
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
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19
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Sher AW, Aufrecht JA, Herrera D, Zimmerman AE, Kim YM, Munoz N, Trejo JB, Paurus VL, Cliff JB, Hu D, Chrisler WB, Tournay RJ, Gomez-Rivas E, Orr G, Ahkami AH, Doty SL. Dynamic nitrogen fixation in an aerobic endophyte of Populus. ISME J 2024; 18:wrad012. [PMID: 38365250 PMCID: PMC10833079 DOI: 10.1093/ismejo/wrad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/11/2023] [Accepted: 11/21/2023] [Indexed: 02/18/2024]
Abstract
Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.
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Affiliation(s)
- Andrew W Sher
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Jayde A Aufrecht
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Daisy Herrera
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Amy E Zimmerman
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Nathalie Munoz
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Jesse B Trejo
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Vanessa L Paurus
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - John B Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - William B Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Robert J Tournay
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Emma Gomez-Rivas
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Sharon L Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
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20
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Kolan D, Cattan-Tsaushu E, Enav H, Freiman Z, Malinsky-Rushansky N, Ninio S, Avrani S. Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality. ISME J 2024; 18:wrad008. [PMID: 38365231 PMCID: PMC10811720 DOI: 10.1093/ismejo/wrad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 02/18/2024]
Abstract
Harmful blooms caused by diazotrophic (nitrogen-fixing) Cyanobacteria are becoming increasingly frequent and negatively impact aquatic environments worldwide. Cyanophages (viruses infecting Cyanobacteria) can potentially regulate cyanobacterial blooms, yet Cyanobacteria can rapidly acquire mutations that provide protection against phage infection. Here, we provide novel insights into cyanophage:Cyanobacteria interactions by characterizing the resistance to phages in two species of diazotrophic Cyanobacteria: Nostoc sp. and Cylindrospermopsis raciborskii. Our results demonstrate that phage resistance is associated with a fitness tradeoff by which resistant Cyanobacteria have reduced ability to fix nitrogen and/or to survive nitrogen starvation. Furthermore, we use whole-genome sequence analysis of 58 Nostoc-resistant strains to identify several mutations associated with phage resistance, including in cell surface-related genes and regulatory genes involved in the development and function of heterocysts (cells specialized in nitrogen fixation). Finally, we employ phylogenetic analyses to show that most of these resistance genes are accessory genes whose evolution is impacted by lateral gene transfer events. Together, these results further our understanding of the interplay between diazotrophic Cyanobacteria and their phages and suggest that a tradeoff between phage resistance and nitrogen fixation affects the evolution of cell surface-related genes and of genes involved in heterocyst differentiation and nitrogen fixation.
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Affiliation(s)
- Dikla Kolan
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3103301, Israel
| | - Esther Cattan-Tsaushu
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3103301, Israel
| | - Hagay Enav
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3103301, Israel
| | - Zohar Freiman
- Kinneret Limnological Laboratory (KLL) Israel Oceanographic and Limnological Research (IOLR), Migdal 1495000, Israel
| | - Nechama Malinsky-Rushansky
- Kinneret Limnological Laboratory (KLL) Israel Oceanographic and Limnological Research (IOLR), Migdal 1495000, Israel
| | - Shira Ninio
- Kinneret Limnological Laboratory (KLL) Israel Oceanographic and Limnological Research (IOLR), Migdal 1495000, Israel
| | - Sarit Avrani
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3103301, Israel
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21
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Laffont C, Frugier F. Rhizobium symbiotic efficiency meets CEP signaling peptides. New Phytol 2024; 241:24-27. [PMID: 37924218 DOI: 10.1111/nph.19367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/13/2023] [Indexed: 11/06/2023]
Abstract
C-terminally encoded peptides (CEP) signaling peptides are drivers of systemic pathways regulating nitrogen (N) acquisition in different plants, from Arabidopsis to legumes, depending on mineral N availability (e.g. nitrate) and on the whole plant N demand. Recent studies in the Medicago truncatula model legume revealed how root-produced CEP peptides control the root competence for endosymbiosis with N fixing rhizobia soil bacteria through the activity of the Compact Root Architecture 2 (CRA2) CEP receptor in shoots. Among CEP genes, MtCEP7 was shown to be tightly linked to nodulation, and the dynamic temporal regulation of its expression reflects the plant ability to maintain a different symbiotic root competence window depending on the symbiotic efficiency of the rhizobium strain, as well as to reinitiate a new window of root competence for nodulation.
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Affiliation(s)
- Carole Laffont
- Institute of Plant Sciences Paris Saclay (IPS2), CNRS, Paris-Saclay University, Paris-Cité University, INRAE, Univ d'Evry, Bat. 630, Avenue des Sciences, Gif-sur-Yvette, 91190, France
| | - Florian Frugier
- Institute of Plant Sciences Paris Saclay (IPS2), CNRS, Paris-Saclay University, Paris-Cité University, INRAE, Univ d'Evry, Bat. 630, Avenue des Sciences, Gif-sur-Yvette, 91190, France
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22
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Roda C, Clúa J, Eylenstein A, Greco M, Ariel F, Zanetti ME, Blanco FA. The C subunit of the nuclear factor Y binds to the Cyclin P4;1 promoter to modulate nodule organogenesis and infection during symbiosis in Phaseolus vulgaris. New Phytol 2024; 241:525-531. [PMID: 38009979 DOI: 10.1111/nph.19419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023]
Affiliation(s)
- Carla Roda
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT-La Plata, CONICET, La Plata, 1900, Argentina
| | - Joaquín Clúa
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT-La Plata, CONICET, La Plata, 1900, Argentina
| | - Andrés Eylenstein
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT-La Plata, CONICET, La Plata, 1900, Argentina
| | - Micaela Greco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT-La Plata, CONICET, La Plata, 1900, Argentina
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CCT Santa Fe, CONICET-Universidad Nacional del Litoral, Santa Fe, 3000, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT-La Plata, CONICET, La Plata, 1900, Argentina
| | - Flavio Antonio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT-La Plata, CONICET, La Plata, 1900, Argentina
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23
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Navarro-Gómez C, León-Mediavilla J, Küpper H, Rodríguez-Simón M, Paganelli-López A, Wen J, Burén S, Mysore KS, Bokhari SNH, Imperial J, Escudero V, González-Guerrero M. Nodule-specific Cu + -chaperone NCC1 is required for symbiotic nitrogen fixation in Medicago truncatula root nodules. New Phytol 2024; 241:793-810. [PMID: 37915139 DOI: 10.1111/nph.19360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023]
Abstract
Cu+ -chaperones are a diverse group of proteins that allocate Cu+ ions to specific copper proteins, creating different copper pools targeted to specific physiological processes. Symbiotic nitrogen fixation carried out in legume root nodules indirectly requires relatively large amounts of copper, for example for energy delivery via respiration, for which targeted copper deliver systems would be required. MtNCC1 is a nodule-specific Cu+ -chaperone encoded in the Medicago truncatula genome, with a N-terminus Atx1-like domain that can bind Cu+ with picomolar affinities. MtNCC1 is able to interact with nodule-specific Cu+ -importer MtCOPT1. MtNCC1 is expressed primarily from the late infection zone to the early fixation zone and is located in the cytosol, associated with plasma and symbiosome membranes, and within nuclei. Consistent with its key role in nitrogen fixation, ncc1 mutants have a severe reduction in nitrogenase activity and a 50% reduction in copper-dependent cytochrome c oxidase activity. A subset of the copper proteome is also affected in the ncc1 mutant nodules. Many of these proteins can be pulled down when using a Cu+ -loaded N-terminal MtNCC1 moiety as a bait, indicating a role in nodule copper homeostasis and in copper-dependent physiological processes. Overall, these data suggest a pleiotropic role of MtNCC1 in copper delivery for symbiotic nitrogen fixation.
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Affiliation(s)
- Cristina Navarro-Gómez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Javier León-Mediavilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Hendrik Küpper
- Laboratory of Plant Biophysics and Biochemistry, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, 37005, Czech Republic
- Department of Experimental Plant Biology, Faculty of Sciences, University of South Bohemia, Ceske Budejovice, 37005, Czech Republic
| | - Mario Rodríguez-Simón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Alba Paganelli-López
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Department of Biotechnology-Plant Biology, Escuela Técnica Superior de Ingeniería Agraria, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Department of Biotechnology-Plant Biology, Escuela Técnica Superior de Ingeniería Agraria, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Kirankumar S Mysore
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Syed Nadeem Hussain Bokhari
- Laboratory of Plant Biophysics and Biochemistry, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, 37005, Czech Republic
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Viviana Escudero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Department of Biotechnology-Plant Biology, Escuela Técnica Superior de Ingeniería Agraria, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, 28040, Spain
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24
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Liu Y, Gao H, Liu S, Li J, Kong F. Synthesizing a Water-Soluble Polymeric Nitrification Inhibitor with Novel Soil-Loosening Ability. Polymers (Basel) 2023; 16:107. [PMID: 38201772 PMCID: PMC10780483 DOI: 10.3390/polym16010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/14/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Nitrification inhibitor is essential for increasing the nitrogen utilization efficiency of agricultural plants, thus reducing environmental pollution and increasing crop yield. However, the easy volatilization and limited functional property is still the bottleneck of nitrification inhibitors. Herein, a novel water-soluble polymeric nitrification inhibitor was synthesized through the copolymerization of acrylamide and bio-based acrylic acid, which was synthesized from biomass-derived furfural, and the complexation of carboxyl groups and 3,4-dimethylpyrazole. The results showed that the nitrification inhibitor was an amorphous polymer product with a glass transition temperature of 146 °C and a thermal decomposition temperature of 176 °C, and the content of 3,4-dimethylpyrazole reached 2.81 wt%, which was 115% higher than our earlier product (1.31 wt%). The polymeric nitrification inhibitor can inhibit the activity of ammonia-oxidizing bacteria effectively, thus inhibiting the conversion of ammonium nitrogen to nitrate nitrogen and converting the insoluble phosphate into soluble and absorbable phosphate. By introducing a copolymer structure with a strong flocculation capacity, the polymeric nitrification inhibitor is further endowed with a soil-loosening function, which can increase the porosity of soil to improve the soil environment. Therefore, the nitrification inhibitor can be used in water-soluble and liquid fertilizers, as well as in high tower melting granulated compound fertilizers.
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Affiliation(s)
- Yu Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China (F.K.)
| | - Hui Gao
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China (F.K.)
- Key Laboratory of Paper Science and Technology of Ministry of Education, Faculty of Light Industry, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Shanshan Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China (F.K.)
- Key Laboratory of Paper Science and Technology of Ministry of Education, Faculty of Light Industry, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Jinrong Li
- School of Mechanical Engineering, Hebei University of Technology, Tianjin 300401, China;
| | - Fangong Kong
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China (F.K.)
- Key Laboratory of Paper Science and Technology of Ministry of Education, Faculty of Light Industry, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
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25
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Huang PW, Tian N, Rajh T, Liu YH, Innocenti G, Sievers C, Medford AJ, Hatzell MC. Formation of Carbon-Induced Nitrogen-Centered Radicals on Titanium Dioxide under Illumination. JACS Au 2023; 3:3283-3289. [PMID: 38155641 PMCID: PMC10751760 DOI: 10.1021/jacsau.3c00556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
Titanium dioxide is the most studied photocatalytic material and has been reported to be active for a wide range of reactions, including the oxidation of hydrocarbons and the reduction of nitrogen. However, the molecular-scale interactions between the titania photocatalyst and dinitrogen are still debated, particularly in the presence of hydrocarbons. Here, we used several spectroscopic and computational techniques to identify interactions among nitrogen, methanol, and titania under illumination. Electron paramagnetic resonance spectroscopy (EPR) allowed us to observe the formation of carbon radicals upon exposure to ultraviolet radiation. These carbon radicals are observed to transform into diazo- and nitrogen-centered radicals (e.g., CHxN2• and CHxNHy•) during photoreaction in nitrogen environment. In situ infrared (IR) spectroscopy under the same conditions revealed C-N stretching on titania. Furthermore, density functional theory (DFT) calculations revealed that nitrogen adsorption and the thermodynamic barrier to photocatalytic nitrogen fixation are significantly more favorable in the presence of hydroxymethyl or surface carbon. These results provide compelling evidence that carbon radicals formed from the photooxidation of hydrocarbons interact with dinitrogen and suggest that the role of carbon-based "hole scavengers" and the inertness of nitrogen atmospheres should be reevaluated in the field of photocatalysis.
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Affiliation(s)
- Po-Wei Huang
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nianhan Tian
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Tijana Rajh
- School
of Molecular Science, Arizona State University, Tempe, Arizona 85281, United States
- Center
of Nanoscale Materials, Argonne National Laboratory, Woodridge, Illinois 60517, United States
| | - Yu-Hsuan Liu
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Giada Innocenti
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Carsten Sievers
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andrew J. Medford
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Marta C. Hatzell
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George
W .Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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26
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Koedooder C, Zhang F, Wang S, Basu S, Haley ST, Tolic N, Nicora CD, Glavina del Rio T, Dyhrman ST, Gledhill M, Boiteau RM, Rubin-Blum M, Shaked Y. Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia. mSystems 2023; 8:e0074223. [PMID: 37916816 PMCID: PMC10734445 DOI: 10.1128/msystems.00742-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/21/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Colonies of the cyanobacteria Trichodesmium act as a biological hotspot for the usage and recycling of key resources such as C, N, P, and Fe within an otherwise oligotrophic environment. While Trichodesmium colonies are known to interact and support a unique community of algae and particle-associated microbes, our understanding of the taxa that populate these colonies and the gene functions they encode is still limited. Characterizing the taxa and adaptive strategies that influence consortium physiology and its concomitant biogeochemistry is critical in a future ocean predicted to have increasingly resource-depleted regions.
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Affiliation(s)
- Coco Koedooder
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Futing Zhang
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Siyuan Wang
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Subhajit Basu
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- Microsensor Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sheean T. Haley
- Lamont-Doherty Earth Observatory, Columbia University, New York, USA
| | - Nikola Tolic
- Earth and Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D. Nicora
- Earth and Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tijana Glavina del Rio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sonya T. Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, New York, USA
- Department of Earth and Environmental Sciences, Columbia University, New York, USA
| | | | - Rene M. Boiteau
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA
| | | | - Yeala Shaked
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
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27
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Yuan Y, Chen Z, Huang X, Wang F, Guo H, Huang Z, Yang H. Comparative analysis of nitrogen content and its influence on actinorhizal nodule and rhizospheric microorganism diversity in three Alnus species. Front Microbiol 2023; 14:1230170. [PMID: 38169791 PMCID: PMC10758417 DOI: 10.3389/fmicb.2023.1230170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Alnus spp. (alder) are typical nonleguminous nitrogen-fixing trees that have a symbiotic relationship with Frankia. To explore the differences in nitrogen-fixing microorganisms between three alders (A. cremastogyne, A. glutinosa, and A. formosana) with different chromosome ploidies, the community structure and compositional diversity of potential nitrogen-fixing microorganism in root nodules and rhizosphere soil were comparatively analyzed using 16S rRNA and nitrogenase (nifH) gene sequencing. The nitrogen contents in the root nodules and rhizosphere soil were also determined. The results showed that the contents of total nitrogen and nitrate nitrogen in the root nodules of the three alders are significantly higher than those in the rhizosphere soils, while the ammonium nitrogen content show the opposite trend. The family, genus, and species levels showed obviously differences between root nodules and rhizosphere soils, while there were no significant differences at the classification level between the three alders. At the phylum level, the dominant phyla from 16S rRNA and nifH gene data in the root nodules and rhizosphere soil of the three alders are phylum Actinomycetota and phylum Pseudomonadota, respectively. The LEfSe results showed that there are significant differences in the dominant groups in the root nodules and rhizosphere oil of the three alders. The relative abundances of dominant groups also showed obvious differences between the root nodules and rhizosphere soils of three alders. The relative abundances of Frankia and unclassified_Frankia in root nodules are obviously higher than those in rhizosphere soils, and their relative abundances in A. glutinosa root nodules are significantly higher than those in A. cremastogyne and A. formosana at the genus and species levels. The diversity of potential nitrogen-fixing microorganism from 16S rRNA and nifH gene data in the A. glutinosa root nodules and rhizosphere soils are all higher than those in A. cremastogyne and A. formosana. The results of functional prediction also showed that the OTUs for nitrogen fixation, nitrate respiration, and ureolysis in A. glutinosa root nodules are higher than those in the other two alders. Redundancy analysis revealed that the total nitrogen content mostly affects the Frankia community. Overall, there are significant differences in the community composition and structure of potential nitrogen-fixing microorganism in the root nodules and rhizosphere soils between the three alders. A. glutinosa showed a relatively stronger nitrogen fixation capacity than A. formosana and A. cremastogyne. The results help elucidates how the community structure and nitrogen-fixing ability of potential nitrogen-fixing microorganism differ between alder species and serve as a reference for applying Frankia to alder plantations.
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Affiliation(s)
- Yuwei Yuan
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Zhi Chen
- Sichuan Key Laboratory of Ecological Restoration and Conservation for Forest and Wetland, Sichuan Academy of Forestry, Chengdu, China
| | - Xin Huang
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Fang Wang
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Hongying Guo
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Zhen Huang
- Sichuan Key Laboratory of Ecological Restoration and Conservation for Forest and Wetland, Sichuan Academy of Forestry, Chengdu, China
| | - Hanbo Yang
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
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Shumilina J, Soboleva A, Abakumov E, Shtark OY, Zhukov VA, Frolov A. Signaling in Legume-Rhizobia Symbiosis. Int J Mol Sci 2023; 24:17397. [PMID: 38139226 PMCID: PMC10743482 DOI: 10.3390/ijms242417397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/19/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
Legumes represent an important source of food protein for human nutrition and animal feed. Therefore, sustainable production of legume crops is an issue of global importance. It is well-known that legume-rhizobia symbiosis allows an increase in the productivity and resilience of legume crops. The efficiency of this mutualistic association strongly depends on precise regulation of the complex interactions between plant and rhizobia. Their molecular dialogue represents a complex multi-staged process, each step of which is critically important for the overall success of the symbiosis. In particular, understanding the details of the molecular mechanisms behind the nodule formation and functioning might give access to new legume cultivars with improved crop productivity. Therefore, here we provide a comprehensive literature overview on the dynamics of the signaling network underlying the development of the legume-rhizobia symbiosis. Thereby, we pay special attention to the new findings in the field, as well as the principal directions of the current and prospective research. For this, here we comprehensively address the principal signaling events involved in the nodule inception, development, functioning, and senescence.
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Affiliation(s)
- Julia Shumilina
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
| | - Alena Soboleva
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| | - Evgeny Abakumov
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| | - Oksana Y. Shtark
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (O.Y.S.); (V.A.Z.)
| | - Vladimir A. Zhukov
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (O.Y.S.); (V.A.Z.)
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
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29
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Nehring L, Kranabetter JM, Harper GJ, Hawkins BJ. Tree-ring δ15N as an indicator of nitrogen dynamics in stands with N2-fixing Alnus rubra. Tree Physiol 2023; 43:2064-2075. [PMID: 37672228 DOI: 10.1093/treephys/tpad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/14/2023] [Accepted: 09/03/2023] [Indexed: 09/07/2023]
Abstract
Tree-ring δ15N may depict site-specific, long-term patterns in nitrogen (N) dynamics under N2-fixing species, but field trials with N2-fixing tree species are lacking and the relationship of temporal patterns in tree-ring δ15N to soil N dynamics is controversial. We examined whether the tree-ring δ15N of N2-fixing red alder (Alnus rubra Bong.) would mirror N accretion rates and δ15N of soils and whether the influence of alder-fixed N could be observed in the wood of a neighboring conifer. We sampled a 27-year-old replacement series trial on south-eastern Vancouver Island, with red alder and coastal Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) planted in five proportions (0/100, 11/89, 25/75, 50/50 and 100/0) at a uniform stem density. An escalation in forest floor N content was evident with an increasing proportion of red alder, equivalent to a difference of ~750 kg N ha-1 between 100% Douglas-fir versus 100% alder. The forest floor horizon also had high δ15N values in treatments with more red alder. Red alder had a consistent quadratic fit in tree-ring δ15N over time, with a net increase of $\sim$1.5‰, on average, from initial values, followed by a plateau or slight decline. Douglas-fir tree-ring δ15N, in contrast, was largely unchanged over time (in three of four plots) but was significantly higher in the 50/50 mix. The minor differences in current leaf litter N content and δ15N between alder and Douglas-fir, coupled with declining growth in red alder, suggests the plateau or declining trend in alder tree-ring δ15N could coincide with lower N2-fixation rates, potentially by loss in alder vigor at canopy closure, or down-regulation via nitrate availability.
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Affiliation(s)
- L Nehring
- Centre for Forest Biology, University of Victoria, PO Box 3020, STN CSC, 3800 Finnerty Road,Victoria, British Columbia V8P 5C2, Canada
| | - J M Kranabetter
- British Columbia Ministry of Forests, PO Box 9536, Stn Prov Govt, 4300 North Road, Victoria, British Columbia V8Z 5J3, Canada
| | - G J Harper
- British Columbia Ministry of Forests, 4th Floor - 545 Superior Street, Victoria, British Columbia V8V 1T7, Canada
| | - B J Hawkins
- Centre for Forest Biology, University of Victoria, PO Box 3020, STN CSC, 3800 Finnerty Road,Victoria, British Columbia V8P 5C2, Canada
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30
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Li XL, Lv XY, Ji JB, Wang WD, Wang J, Wang C, He HB, Ben AL, Liu TL. Complete genome sequence of Nguyenibacter sp. L1, a phosphate solubilizing bacterium isolated from Lespedeza bicolor rhizosphere. Front Microbiol 2023; 14:1257442. [PMID: 38152372 PMCID: PMC10752598 DOI: 10.3389/fmicb.2023.1257442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023] Open
Abstract
Phosphorus (P) deficiency is a predominant constraint on plant growth in acidified soils, largely due to the sequestration of P by toxic aluminum (Al) compounds. Indigenous phosphorus-solubilizing bacteria (PSBs) capable of mobilizing Al-P in these soils hold significant promise. A novel Al-P-solubilizing strain, Al-P Nguyenibacter sp. L1, was isolated from the rhizosphere soil of healthy Lespedeza bicolor plants indigenous to acidic terrains. However, our understanding of the genomic landscape of bacterial species within the genus Nguyenibacter remains in its infancy. To further explore its biotechnological potentialities, we sequenced the complete genome of this strain, employing an amalgamation of Oxford Nanopore ONT and Illumina sequencing platforms. The resultant genomic sequence of Nguyenibacter sp. L1 manifests as a singular, circular chromosome encompassing 4,294,433 nucleotides and displaying a GC content of 66.73%. The genome was found to host 3,820 protein-coding sequences, 12 rRNAs, and 55 tRNAs. Intriguingly, annotations derived from the eggNOG and KEGG databases indicate the presence of genes affiliated with phosphorus solubilization and nitrogen fixation, including iscU, glnA, and gltB/D associated with nitrogen fixation, and pqqBC associated with inorganic phosphate dissolution. Several bioactive secondary metabolite genes in the genome, including pqqCDE, phytoene synthase and squalene synthase predicted by antiSMASH. Moreover, we uncovered a complete metabolic pathway for ammonia, suggesting an ammonia-affinity property inherent to Nguyenibacter sp. L1. This study verifies the nitrogen-fixing and phosphate-dissolving abilities of Nguyenibacter sp. L1 at the molecular level through genetic screening and analysis. The insights gleaned from this study offer strategic guidance for future strain enhancement and establish a strong foundation for the potential incorporation of this bacterium into agricultural practices.
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Affiliation(s)
- Xiao Li Li
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Xin Yang Lv
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Jun Bin Ji
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Wei Duo Wang
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Ji Wang
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Cong Wang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Hai Bin He
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ai Ling Ben
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Ting Li Liu
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
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Sharma M, Kumar A, Gill D, Jaiswal S, Patra A, Bhattacharya S, Krishnan V. Boosting Photocatalytic Nitrogen Fixation via Nanoarchitectonics Using Oxygen Vacancy Regulation in W-Doped Bi 2MoO 6 Nanosheets. ACS Appl Mater Interfaces 2023; 15:55765-55778. [PMID: 37975858 DOI: 10.1021/acsami.3c12563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Ammonia and nitrates are key raw materials for various chemical and pharmaceutical industries. The conventional methods like Haber-Bosch and Ostwald methods used in the synthesis of ammonia and nitrates, respectively, result in harmful emission of gases. In recent years, the photocatalytic fixation of N2 into NH3 and nitrates has become a hot topic since it is a green and cost-effective approach. However, the simultaneous production of ammonia and nitrates has not been studied much. In this regard, we have synthesized W-doped Bi2MoO6 nanosheets in various molar ratios and demonstrated their potential as efficient photocatalysts for the simultaneous production of NH3 and NO3- ions under visible light irradiation. It was found that one of the catalysts (BMWO0.4) having an optimal molar ratio of doped tungsten showed the best photocatalytic NH3 production (56 μmol h-1) without using any sacrificial agents along with the simultaneous production of NO3- ions at a rate of 7 μmol h-1. The enhanced photocatalytic activity of the synthesized photocatalysts could be ascribed to oxygen vacancy defects caused by Mo substitution by a more electronegative W atom. Furthermore, density functional theory calculations verified the alteration in the band gap after doping of W atoms and also showed a strong chemisorption of N2 over the photocatalyst surface leading to its activation and thereby enhancing the photocatalytic activity. Thus, the present work provides insights into the effect of structural distortions on tailoring the efficiency of materials used in photocatalytic N2 fixation.
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Affiliation(s)
- Manisha Sharma
- School of Chemical Sciences and Advanced Materials Research Center, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175075, India
| | - Ashish Kumar
- Department of Chemistry, Sardar Patel University Mandi, Mandi, Himachal Pradesh 175001, India
| | - Deepika Gill
- Department of Physics, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shilpi Jaiswal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Abhijit Patra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Saswata Bhattacharya
- Department of Physics, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Venkata Krishnan
- School of Chemical Sciences and Advanced Materials Research Center, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175075, India
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Warmack RA, Rees DC. Nitrogenase beyond the Resting State: A Structural Perspective. Molecules 2023; 28:7952. [PMID: 38138444 PMCID: PMC10745740 DOI: 10.3390/molecules28247952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Nitrogenases have the remarkable ability to catalyze the reduction of dinitrogen to ammonia under physiological conditions. How does this happen? The current view of the nitrogenase mechanism focuses on the role of hydrides, the binding of dinitrogen in a reductive elimination process coupled to loss of dihydrogen, and the binding of substrates to a binuclear site on the active site cofactor. This review focuses on recent experimental characterizations of turnover relevant forms of the enzyme determined by cryo-electron microscopy and other approaches, and comparison of these forms to the resting state enzyme and the broader family of iron sulfur clusters. Emerging themes include the following: (i) The obligatory coupling of protein and electron transfers does not occur in synthetic and small-molecule iron-sulfur clusters. The coupling of these processes in nitrogenase suggests that they may involve unique features of the cofactor, such as hydride formation on the trigonal prismatic arrangement of irons, protonation of belt sulfurs, and/or protonation of the interstitial carbon. (ii) Both the active site cofactor and protein are dynamic under turnover conditions; the changes are such that more highly reduced forms may differ in key ways from the resting-state structure. Homocitrate appears to play a key role in coupling cofactor and protein dynamics. (iii) Structural asymmetries are observed in nitrogenase under turnover-relevant conditions by cryo-electron microscopy, although the mechanistic relevance of these states (such as half-of-sites reactivity) remains to be established.
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Affiliation(s)
- Rebeccah A. Warmack
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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33
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Timofeeva AM, Galyamova MR, Sedykh SE. Plant Growth-Promoting Soil Bacteria: Nitrogen Fixation, Phosphate Solubilization, Siderophore Production, and Other Biological Activities. Plants (Basel) 2023; 12:4074. [PMID: 38140401 PMCID: PMC10748132 DOI: 10.3390/plants12244074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
This review covers the literature data on plant growth-promoting bacteria in soil, which can fix atmospheric nitrogen, solubilize phosphates, produce and secrete siderophores, and may exhibit several different behaviors simultaneously. We discuss perspectives for creating bacterial consortia and introducing them into the soil to increase crop productivity in agrosystems. The application of rhizosphere bacteria-which are capable of fixing nitrogen, solubilizing organic and inorganic phosphates, and secreting siderophores, as well as their consortia-has been demonstrated to meet the objectives of sustainable agriculture, such as increasing soil fertility and crop yields. The combining of plant growth-promoting bacteria with mineral fertilizers is a crucial trend that allows for a reduction in fertilizer use and is beneficial for crop production.
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Affiliation(s)
- Anna M. Timofeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Maria R. Galyamova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Sergey E. Sedykh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
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Einsle O. On the Shoulders of Giants-Reaching for Nitrogenase. Molecules 2023; 28:7959. [PMID: 38138449 PMCID: PMC10745432 DOI: 10.3390/molecules28247959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Only a single enzyme system-nitrogenase-carries out the conversion of atmospheric N2 into bioavailable ammonium, an essential prerequisite for all organismic life. The reduction of this inert substrate at ambient conditions poses unique catalytic challenges that strain our mechanistic understanding even after decades of intense research. Structural biology has added its part to this greater tapestry, and in this review, I provide a personal (and highly biased) summary of the parts of the story to which I had the privilege to contribute. It focuses on the crystallographic analysis of the three isoforms of nitrogenases at high resolution and the binding of ligands and inhibitors to the active-site cofactors of the enzyme. In conjunction with the wealth of available biochemical, biophysical, and spectroscopic data on the protein, this has led us to a mechanistic hypothesis based on an elementary mechanism of repetitive hydride formation and insertion.
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Affiliation(s)
- Oliver Einsle
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany
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35
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Lee WH, Yoon CK, Park H, Park GH, Jeong JH, Cha GD, Lee BH, Lee J, Lee CW, Bootharaju MS, Sunwoo SH, Ryu J, Lee C, Cho YJ, Nam TW, Ahn KH, Hyeon T, Seok YJ, Kim DH. Highly Efficient Nitrogen-Fixing Microbial Hydrogel Device for Sustainable Solar Hydrogen Production. Adv Mater 2023; 35:e2306092. [PMID: 37739451 DOI: 10.1002/adma.202306092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/20/2023] [Indexed: 09/24/2023]
Abstract
Conversion of sunlight and organic carbon substrates to sustainable energy sources through microbial metabolism has great potential for the renewable energy industry. Despite recent progress in microbial photosynthesis, the development of microbial platforms that warrant efficient and scalable fuel production remains in its infancy. Efficient transfer and retrieval of gaseous reactants and products to and from microbes are particular hurdles. Here, inspired by water lily leaves floating on water, a microbial device designed to operate at the air-water interface and facilitate concomitant supply of gaseous reactants, smooth capture of gaseous products, and efficient sunlight delivery is presented. The floatable device carrying Rhodopseudomonas parapalustris, of which nitrogen fixation activity is first determined through this study, exhibits a hydrogen production rate of 104 mmol h-1 m-2 , which is 53 times higher than that of a conventional device placed at a depth of 2 cm in the medium. Furthermore, a scaled-up device with an area of 144 cm2 generates hydrogen at a high rate of 1.52 L h-1 m-2 . Efficient nitrogen fixation and hydrogen generation, low fabrication cost, and mechanical durability corroborate the potential of the floatable microbial device toward practical and sustainable solar energy conversion.
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Affiliation(s)
- Wang Hee Lee
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang-Kyu Yoon
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyunseo Park
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ga-Hee Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae Hwan Jeong
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Gi Doo Cha
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byoung-Hoon Lee
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Juri Lee
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chan Woo Lee
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Megalamane S Bootharaju
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung-Hyuk Sunwoo
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jaeyune Ryu
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Changha Lee
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yong-Joon Cho
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
- Multidimensional Genomics Research Center, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Tae-Wook Nam
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
- MightyBugs, Inc., Busan, 46918, Republic of Korea
| | - Kyung Hyun Ahn
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Taeghwan Hyeon
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yeong-Jae Seok
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dae-Hyeong Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
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36
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Zhu YG, Peng J, Chen C, Xiong C, Li S, Ge A, Wang E, Liesack W. Harnessing biological nitrogen fixation in plant leaves. Trends Plant Sci 2023; 28:1391-1405. [PMID: 37270352 DOI: 10.1016/j.tplants.2023.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/05/2023]
Abstract
The importance of biological nitrogen fixation (BNF) in securing food production for the growing world population with minimal environmental cost has been increasingly acknowledged. Leaf surfaces are one of the biggest microbial habitats on Earth, harboring diverse free-living N2-fixers. These microbes inhabit the epiphytic and endophytic phyllosphere and contribute significantly to plant N supply and growth. Here, we summarize the contribution of phyllosphere-BNF to global N cycling, evaluate the diversity of leaf-associated N2-fixers across plant hosts and ecosystems, illustrate the ecological adaptation of N2-fixers to the phyllosphere, and identify the environmental factors driving BNF. Finally, we discuss potential BNF engineering strategies to improve the nitrogen uptake in plant leaves and thus sustainable food production.
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Affiliation(s)
- Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Jingjing Peng
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Cai Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Shule Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Anhui Ge
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
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Ding Y, Bertram JR, Nagpal P. Utilizing Atmospheric Carbon Dioxide and Sunlight in Graphene Quantum Dot-Based Nano-Biohybrid Organisms for Making Carbon-Negative and Carbon-Neutral Products. ACS Appl Mater Interfaces 2023; 15:53464-53475. [PMID: 37953629 DOI: 10.1021/acsami.3c12524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Increasing emissions of greenhouse gases compounded with legacy emissions in the earth's atmosphere poses an existential threat to human survival. One potential solution is creating carbon-negative and carbon-neutral materials, specifically for commodities used heavily throughout the globe, using a low-cost, scalable, and technologically and economically feasible process that can be deployed without the need for extensive infrastructure or skill requirements. Here, we demonstrate that nickel-functionalized graphene quantum dots (GQDs) can effectively couple to nonphotosynthetic bacteria at a cellular, molecular, and optoelectronic level, creating nanobiohybrid organisms (nanorgs) that enable the utilization of sunlight to convert carbon dioxide, air, and water into high-value-added chemicals such as ammonia (NH3), ethylene (C2H4), isopropanol (IPA), 2,3-butanediol (BDO), C11-C15 methyl ketones (MKs), and degradable bioplastics poly hydroxybutyrate (PHB) with high efficiency and selectivity. We demonstrate a high turnover number (TON) of up to 108 (mol of product per mol of cells), ease of application, facile scalability (demonstrated using a 30 L tank in a lab), and sustainable generation of carbon nanomaterials from recovered bacteria for creating nanorgs without the use of any toxic chemicals or materials. These findings can have important implications for the further development of sustainable processes for making carbon-negative materials using nanorgs.
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Affiliation(s)
- Yuchen Ding
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - John R Bertram
- Materials Science and Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
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Gao J, Wu F, Zhao Y, Bian X, Zhou C, Tang J, Zhang T. Tuning the Interfaces of ZnO/ZnCr 2 O 4 Derived from Layered-Double-Hydroxide Precursors to Advance Nitrogen Photofixation. ChemSusChem 2023; 16:e202300944. [PMID: 37528771 DOI: 10.1002/cssc.202300944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/03/2023]
Abstract
Drawing inspiration from the enzyme nitrogenase in nature, researchers are increasingly delving into semiconductor photocatalytic nitrogen fixation due to its similar surface catalytic processes. Herein, we reported a facile and efficient approach to achieving the regulation of ZnO/ZnCr2 O4 photocatalysts with ZnCr-layered double hydroxide (ZnCr-LDH) as precursors. By optimizing the composition ratio of Zn/Cr in ZnCr-LDH to tune interfaces, we can achieve an enhanced nitrogen photofixation performance (an ammonia evolution rate of 31.7 μmol g-1 h-1 using pure water as a proton source) under ambient conditions. Further, photo-electrochemical measurements and transient surface photovoltage spectroscopy revealed that the enhanced photocatalytic activity can be ascribed to the effective carrier separation efficiency, originating from the abundant composite interfaces. This work further demonstrated a promising and viable strategy for the synthesis of nanocomposite photocatalysts for nitrogen photofixation and other challenging photocatalytic reactions.
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Affiliation(s)
- Junyu Gao
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Fan Wu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yunxuan Zhao
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- College of Science, Hebei University of Science and Technology, Shijiazhuang, 050018, P. R. China
| | - Xuanang Bian
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Chao Zhou
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Junwang Tang
- Department of Chemical Engineering, University College London, Torrington Place, London, WC1E 7JE, United Kingdom
- Industrial Catalysis Center, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Tierui Zhang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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Hu Y, Chen Y, Yang X, Deng L, Lu X. Enhancing Soybean Yield: The Synergy of Sulfur and Rhizobia Inoculation. Plants (Basel) 2023; 12:3911. [PMID: 38005808 PMCID: PMC10675423 DOI: 10.3390/plants12223911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023]
Abstract
Sulfur deficiency severely limits soybean growth, inhibiting the rhizobia nitrogenase and soybean protein synthesis. This study assessed the impact of sulfur fertilization and rhizobia inoculation on soybean growth and nitrogen fixation through bacterial culture and hydroponic experiments. We selected three rhizobia strains for bacterial cultures and used six sulfur levels. The test demonstrated severe inhibition of Rhizobium USDA110 growth without sulfur. In hydroponic experiment, we employed five sulfur levels with USDA110 as the inoculum strain. Soybean growth, nitrogen fixation, yield, and root morphology-related parameters, and root nodule growth, were significantly inhibited without sulfur. Following Rhizobium inoculation, low sulfur concentrations (0.15-0.60 mM) stimulated early-stage (V9) root growth and increased shoot nitrogen accumulation, but inhibited root growth at R5 stage. Furthermore, Rhizobium inoculation notably enhanced soybean growth, nitrogen fixation, and yield, especially within the recommended low sulfur concentration range (0.15-0.30 mM). The maximum nodule nitrogenase activity at R5 stage and highest yield was recorded at a 0.3 mM sulfur concentration with Rhizobium inoculation, which was 9.51-1222.07% higher than other treatments. These findings highlight that low sulfur concentration and rhizobia inoculation enhance soybean growth, nitrogen fixation, and yield but reduce soybean root efficacy, increasing reliance on root nodules.
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Affiliation(s)
- Yiao Hu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (Y.C.); (X.Y.); (X.L.)
- Guangdong Weisheng Liansu Technology Co., Ltd., Foshan 528313, China
| | - Yulin Chen
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (Y.C.); (X.Y.); (X.L.)
| | - Xu Yang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (Y.C.); (X.Y.); (X.L.)
| | - Lansheng Deng
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (Y.C.); (X.Y.); (X.L.)
| | - Xing Lu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (Y.C.); (X.Y.); (X.L.)
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Tort R, Bagger A, Westhead O, Kondo Y, Khobnya A, Winiwarter A, Davies BJV, Walsh A, Katayama Y, Yamada Y, Ryan MP, Titirici MM, Stephens IEL. Searching for the Rules of Electrochemical Nitrogen Fixation. ACS Catal 2023; 13:14513-14522. [PMID: 38026818 PMCID: PMC10660346 DOI: 10.1021/acscatal.3c03951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Li-mediated ammonia synthesis is, thus far, the only electrochemical method for heterogeneous decentralized ammonia production. The unique selectivity of the solid electrode provides an alternative to one of the largest heterogeneous thermal catalytic processes. However, it is burdened with intrinsic energy losses, operating at a Li plating potential. In this work, we survey the periodic table to understand the fundamental features that make Li stand out. Through density functional theory calculations and experimentation on chemistries analogous to lithium (e.g., Na, Mg, Ca), we find that lithium is unique in several ways. It combines a stable nitride that readily decomposes to ammonia with an ideal solid electrolyte interphase, balancing reagents at the reactive interface. We propose descriptors based on simulated formation and binding energies of key intermediates and further on hard and soft acids and bases (HSAB principle) to generalize such features. The survey will help the community toward electrochemical systems beyond Li for nitrogen fixation.
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Affiliation(s)
- Romain Tort
- Department
of Chemical Engineering, Imperial College
London, London SW7 2AZ, U.K.
| | - Alexander Bagger
- Department
of Chemical Engineering, Imperial College
London, London SW7 2AZ, U.K.
- Department
of Physics, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Olivia Westhead
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Yasuyuki Kondo
- Osaka
University, SANKEN (The Institute of Scientific and Industrial Research),
Mihogaoka, Osaka, Ibaraki 567-0047, Japan
| | - Artem Khobnya
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Anna Winiwarter
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | | | - Aron Walsh
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Yu Katayama
- Osaka
University, SANKEN (The Institute of Scientific and Industrial Research),
Mihogaoka, Osaka, Ibaraki 567-0047, Japan
| | - Yuki Yamada
- Osaka
University, SANKEN (The Institute of Scientific and Industrial Research),
Mihogaoka, Osaka, Ibaraki 567-0047, Japan
| | - Mary P. Ryan
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
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Turk-Kubo KA, Gradoville MR, Cheung S, Cornejo-Castillo FM, Harding KJ, Morando M, Mills M, Zehr JP. Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters. FEMS Microbiol Rev 2023; 47:fuac046. [PMID: 36416813 PMCID: PMC10719068 DOI: 10.1093/femsre/fuac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/17/2023] Open
Abstract
Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Mary R Gradoville
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Columbia River Inter-Tribal Fish Commission, Portland, OR, United States
| | - Shunyan Cheung
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Francisco M Cornejo-Castillo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Pg. Marítim Barceloneta, 37-49 08003 Barcelona, Spain
| | - Katie J Harding
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Marine Biology Research Division, Scripps Institute of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Michael Morando
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Matthew Mills
- Department of Earth System Science, Stanford University, 473 Via Ortega, Stanford, CA 94305, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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Xing WY, Liu J, Zhang CC. HetF defines a transition point from commitment to morphogenesis during heterocyst differentiation in the cyanobacterium Anabaena sp. PCC 7120. Mol Microbiol 2023; 120:740-753. [PMID: 37804047 DOI: 10.1111/mmi.15177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023]
Abstract
The filamentous cyanobacterium Anabaena sp. PCC 7120 is able to form heterocysts for nitrogen fixation. Heterocyst differentiation is initiated by combined-nitrogen deprivation, followed by the commitment step during which the developmental process becomes irreversible. Mature heterocysts are terminally differentiated cells unable to divide, and cell division is required for heterocyst differentiation. Previously, we have shown that the HetF protease regulates cell division and heterocyst differentiation by cleaving PatU3, which is an inhibitor for both events. When hetF is required during the developmental program remains unknown. Here, by controlling the timing of hetF expression during heterocyst differentiation, we provide evidence that hetF is required just before the beginning of heterocyst morphogenesis. Consistent with this finding, transcriptome data show that most of the genes known to be involved in the early step (such as hetR and ntcA) or the commitment step (such as hetP and hetZ) of heterocyst development could be expressed in the ΔhetF mutant. In contrast, most of the genes involved in heterocyst morphogenesis and nitrogen fixation remain repressed in the mutant. These results indicated that in the absence of hetF, heterocyst differentiation is able to be initiated and proceeds to the stage just before heterocyst envelope formation.
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Affiliation(s)
- Wei-Yue Xing
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Jing Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Cheng-Cai Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
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Thapa L, Retna Raj C. Nitrogen Electrocatalysis: Electrolyte Engineering Strategies to Boost Faradaic Efficiency. ChemSusChem 2023; 16:e202300465. [PMID: 37401159 DOI: 10.1002/cssc.202300465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
The electrochemical activation of dinitrogen at ambient temperature and pressure for the synthesis of ammonia has drawn increasing attention. The faradaic efficiency (FE) as well as ammonia yield in the electrochemical synthesis is far from reaching the requirement of industrial-scale production. In aqueous electrolytes, the competing electron-consuming hydrogen evolution reaction (HER) and poor solubility of nitrogen are the two major bottlenecks. As the electrochemical reduction of nitrogen involves proton-coupled electron transfer reaction, rationally engineered electrolytes are required to boost FE and ammonia yield. In this Review, we comprehensively summarize various electrolyte engineering strategies to boost the FE in aqueous and non-aqueous medium and suggest possible approaches to further improve the performance. In aqueous medium, the performance can be improved by altering the electrolyte pH, transport velocity of protons, and water activity. Other strategies involve the use of hybrid and water-in-salt electrolytes, ionic liquids, and non-aqueous electrolytes. Existing aqueous electrolytes are not ideal for industrial-scale production. Suppression of HER and enhanced nitrogen solubility have been observed with hybrid and non-aqueous electrolytes. The engineered electrolytes are very promising though the electrochemical activation has several challenges. The outcome of lithium-mediated nitrogen reduction reaction with engineered non-aqueous electrolyte is highly encouraging.
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Affiliation(s)
- Loknath Thapa
- Functional Materials and Electrochemistry Lab, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
| | - C Retna Raj
- Functional Materials and Electrochemistry Lab, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
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Liu GH, Yang S, Han S, Xie CJ, Liu X, Rensing C, Zhou SG. Nitrogen fixation and transcriptome of a new diazotrophic Geomonas from paddy soils. mBio 2023; 14:e0215023. [PMID: 37855611 PMCID: PMC10746287 DOI: 10.1128/mbio.02150-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 10/20/2023] Open
Abstract
Nitrogen gas (N2) fixation driven by diazotrophs is a crucial process for supplying nitrogen to paddy soil ecosystems. The genus Geomonas has been considered to be an important potential diazotroph in paddy soils, but direct experimental evidence of the nitrogen-fixing ability of Geomonas in pure culture is still lacking. Hence, we aimed to demonstrate this nitrogen-fixing capability and shed light on how this process was regulated in response to ammonium (NH4 +) in Geomonas. In this study, we determined that a key nitrogenase gene (nifH) was present in 50 isolates from paddy soils. Members of Geomonas contained the minimum nitrogen fixation gene cluster (nifBHDKEN) based on genomic analysis, implying Geomonas species had the potential to fix nitrogen. Acetylene reduction assay (ARA), 15N2 isotope labeling, and total nitrogen accumulation assays validated that Geomonas was, indeed, able to fix nitrogen in pure culture. Under nitrogen-fixing conditions, the cell morphology of Geomonas changed from short rod-shaped (with NH4 +) to long rod-shaped and flagella became longer and thicker. The expression of genes correlated to nitrogen fixation in the Geomonas transcriptome was quantified in response to NH4 +. Expression of genes associated with nitrogenase, flavin-based electron bifurcation complexes (such as the FixAB system), NH4 + uptake, and transformation (e.g., glutamine and glutamate synthetases) were significantly upregulated under nitrogen-fixing conditions, suggesting these mechanisms might be involved in N2 fixation in Geomonas. These results were verified by RT-qPCR. Taken together, our results demonstrate that Geomonas species possess the ability to fix N2 and expand our understanding on the ecological significance and potential applications of Geomonas in paddy soil ecosystems. IMPORTANCE The ability of Geomonas species to fix nitrogen gas (N2) is an important metabolic feature for its application as a plant growth-promoting rhizobacterium. This research is of great importance as it provides the first comprehensive direct experimental evidence of nitrogen fixation by the genus Geomonas in pure culture. We isolated a number of Geomonas strains from paddy soils and determined that nifH was present in these strains. This study demonstrated that these Geomonas species harbored genes encoding nitrogenase, as do Geobacter and Anaeromyxobacter in the same class of Deltaproteobacteria. We demonstrated N2-dependent growth of Geomonas and determined regulation of gene expression associated with nitrogen fixation. The research establishes and advances our understanding of nitrogen fixation in Geomonas.
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Affiliation(s)
- Guo-Hong Liu
- Institute of Resources, Environment and Soil Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou City, Fujian Province, China
| | - Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
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García-Tomsig NI, García-Rodriguez FM, Guedes-García SK, Millán V, Becker A, Robledo M, Jiménez-Zurdo JI. A double-negative feedback loop between NtrBC and a small RNA rewires nitrogen metabolism in legume symbionts. mBio 2023; 14:e0200323. [PMID: 37850753 PMCID: PMC10746234 DOI: 10.1128/mbio.02003-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
The nitrogen (N) status transduced via the NtrBC two-component system is a major signaling cue in the root nodule endosymbiosis of diazotrophic rhizobia with legumes. NtrBC is upregulated in the N-limiting rhizosphere environment at the onset of nodulation but silenced in nodules to favor the assimilation of the fixed N into plant biomass. We reported that the trans-acting sRNA NfeR1 (Nodule Formation Efficiency RNA) broadly influences the symbiotic performance of the α-rhizobium Sinorhizobium meliloti. Here, we show that NfeR1 is indeed an N-responsive sRNA that fine-tunes NtrBC output during the symbiotic transition. Biochemical and genetic approaches unveiled that NtrC and the LysR-type symbiotic regulator LsrB bind at distinct nearby sites in the NfeR1 promoter, acting antagonistically as repressor and activator of transcription, respectively. This complex transcriptional control specifies peak NfeR1 steady-state levels in N-starved and endosymbiotic bacteria. Furthermore, NfeR1 base pairs the translation initiation region of the histidine kinase coding mRNA ntrB, causing a decrease in both NtrB and NtrC abundance as assessed by double-plasmid genetic assays. In the context of endogenous regulation, NfeR1-mediated ntrBC silencing most likely amends the effective strength of the known operon autorepression exerted by NtrC. Accordingly, a lack of NfeR1 shifts the wild-type NtrBC output, restraining the fitness of free-living rhizobia under N stress and plant growth upon nodulation. The mixed NtrBC-NfeR1 double-negative feedback loop is thus an unprecedented adaptive network motif that helps α-rhizobia adjust N metabolism to the demands of an efficient symbiosis with legume plants. IMPORTANCE Root nodule endosymbioses between diazotrophic rhizobia and legumes provide the largest input of combined N to the biosphere, thus representing an alternative to harmful chemical fertilizers for sustainable crop production. Rhizobia have evolved intricate strategies to coordinate N assimilation for their own benefit with N2 fixation to sustain plant growth. The rhizobial N status is transduced by the NtrBC two-component system, the seemingly ubiquitous form of N signal transduction in Proteobacteria. Here, we show that the regulatory sRNA NfeR1 (nodule formation efficiency RNA) of the alfalfa symbiont Sinorhizobium meliloti is transcribed from a complex promoter repressed by NtrC in a N-dependent manner and feedback silences ntrBC by complementary base-pairing. These findings unveil a more prominent role of NtrC as a transcriptional repressor than hitherto anticipated and a novel RNA-based mechanism for NtrBC regulation. The NtrBC-NfeR1 double-negative feedback loop accurately rewires symbiotic S. meliloti N metabolism and is likely conserved in α-rhizobia.
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Affiliation(s)
- Natalia I. García-Tomsig
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Fernando M. García-Rodriguez
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Sabina K. Guedes-García
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Vicenta Millán
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Marta Robledo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - José I. Jiménez-Zurdo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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46
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Granada Agudelo M, Ruiz B, Capela D, Remigi P. The role of microbial interactions on rhizobial fitness. Front Plant Sci 2023; 14:1277262. [PMID: 37877089 PMCID: PMC10591227 DOI: 10.3389/fpls.2023.1277262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023]
Abstract
Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.
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Affiliation(s)
- Margarita Granada Agudelo
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Bryan Ruiz
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Delphine Capela
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Philippe Remigi
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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47
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Mohd-Radzman NA, Drapek C. Compartmentalisation: A strategy for optimising symbiosis and tradeoff management. Plant Cell Environ 2023; 46:2998-3011. [PMID: 36717758 DOI: 10.1111/pce.14553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Plant root architecture is developmentally plastic in response to fluctuating nutrient levels in the soil. Part of this developmental plasticity is the formation of dedicated root cells and organs to host mutualistic symbionts. Structures like nitrogen-fixing nodules serve as alternative nutrient acquisition strategies during starvation conditions. Some root systems can also form myconodules-globular root structures that can host mycorrhizal fungi. The myconodule association is different from the wide-spread arbuscular mycorrhization. This range of symbiotic associations provides different degrees of compartmentalisation, from the cellular to organ scale, which allows the plant host to regulate the entry and extent of symbiotic interactions. In this review, we discuss the degrees of symbiont compartmentalisation by the plant host as a developmental strategy and speculate how spatial confinement mitigates risks associated with root symbiosis.
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Affiliation(s)
| | - Colleen Drapek
- Sainsbury Laboratory Cambridge University (SLCU), Bateman Street, Cambridge, UK
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48
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Holland BL, Matthews ML, Bota P, Sweetlove LJ, Long SP, diCenzo GC. A genome-scale metabolic reconstruction of soybean and Bradyrhizobium diazoefficiens reveals the cost-benefit of nitrogen fixation. New Phytol 2023; 240:744-756. [PMID: 37649265 DOI: 10.1111/nph.19203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/05/2023] [Indexed: 09/01/2023]
Abstract
Nitrogen-fixing symbioses allow legumes to thrive in nitrogen-poor soils at the cost of diverting some photoassimilate to their microsymbionts. Effort is being made to bioengineer nitrogen fixation into nonleguminous crops. This requires a quantitative understanding of its energetic costs and the links between metabolic variations and symbiotic efficiency. A whole-plant metabolic model for soybean (Glycine max) with its associated microsymbiont Bradyrhizobium diazoefficiens was developed and applied to predict the cost-benefit of nitrogen fixation with varying soil nitrogen availability. The model predicted a nitrogen-fixation cost of c. 4.13 g C g-1 N, which when implemented into a crop scale model, translated to a grain yield reduction of 27% compared with a non-nodulating plant receiving its nitrogen from the soil. Considering the lower nitrogen content of cereals, the yield cost to a hypothetical N-fixing cereal is predicted to be less than half that of soybean. Soybean growth was predicted to be c. 5% greater when the nodule nitrogen export products were amides versus ureides. This is the first metabolic reconstruction in a tropical crop species that simulates the entire plant and nodule metabolism. Going forward, this model will serve as a tool to investigate carbon use efficiency and key mechanisms within N-fixing symbiosis in a tropical species forming determinate nodules.
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Affiliation(s)
- Bethany L Holland
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Megan L Matthews
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pedro Bota
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Stephen P Long
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - George C diCenzo
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
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Chanderban M, Hill CA, Dhamad AE, Lessner DJ. Expression of V-nitrogenase and Fe-nitrogenase in Methanosarcina acetivorans is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase. Appl Environ Microbiol 2023; 89:e0103323. [PMID: 37695043 PMCID: PMC10537573 DOI: 10.1128/aem.01033-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/07/2023] [Indexed: 09/12/2023] Open
Abstract
All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N2) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown. Methanosarcina acetivorans contains nif, vnf, and anf gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by M. acetivorans in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the nif, vnf, and/or anf gene clusters. The availability of Mo and V significantly affected growth of M. acetivorans with N2 but not with NH4Cl. M. acetivorans exhibited the fastest growth rate and highest cell yield during growth with N2 in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the nif operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas vnf and anf transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in M. acetivorans is tightly controlled and dependent on Mo-nitrogenase expression. IMPORTANCE Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.
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Affiliation(s)
- Melissa Chanderban
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Christopher A. Hill
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Ahmed E. Dhamad
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
- Department of Biological Sciences, Wasit University, Wasit, Iraq
| | - Daniel J. Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
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50
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Guo DJ, Li DP, Yang B, Verma KK, Singh RK, Singh P, Khan Q, Sharma A, Qin Y, Zhang BQ, Song XP, Li YR. Corrigendum: Effect of endophytic diazotroph Enterobacter roggenkampii ED5 on nitrogen-metabolism-related microecology in the sugarcane rhizosphere at different nitrogen levels. Front Microbiol 2023; 14:1290575. [PMID: 37829447 PMCID: PMC10565565 DOI: 10.3389/fmicb.2023.1290575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2023.1132016.].
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Affiliation(s)
- Dao-Jun Guo
- College of Life Sciences and Engineering, Hexi University, Zhangye, Gansu, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Bin Yang
- College of Life Sciences and Engineering, Hexi University, Zhangye, Gansu, China
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Qaisar Khan
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Ying Qin
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Bao-Qing Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Xiu-Peng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
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