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Li Q, He Y, Feng J, He Y, Zhang S. Pseudomonas fluorescens Inoculation Enhances Salix matsudana Growth by Modifying Phyllosphere Microbiomes, Surpassing Nitrogen Fertilization. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39300758 DOI: 10.1111/pce.15162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 09/22/2024]
Abstract
The enhancement of plant growth by soil fertilization and microbial inoculation involves different mechanisms, particularly by altering the phyllosphere microbiome. This study investigated how nitrogen (N) fertilization, Pseudomonas fluorescens strain R124 inoculation and their combined effects influence the growth of different-aged Salix matsudana cuttings by modulating N dynamics within the phyllosphere microbiome. Results showed that P. fluorescens inoculation was significantly more effective than N fertilization alone, enhancing biomass, plant nutrient uptake, soil nutrient content and root development by 90.51%, 18.18%, 72.74% and 126.20%, respectively. Crucially, the inoculation notably shifted the beta-diversity of the phyllosphere microbial community, with K-strategy fungi enhancing plant N fixation and subsequent plant growth. Cuttings from middle-aged forests displayed more robust growth than those from young-aged, associated with a varied impact on phyllosphere fungi, notably increasing the relative abundance of Myriangiales in young (76.37%) and Capnodiales in middle-aged cuttings (42.37%), which improve phyllosphere stability and plant health. These findings highlight the effectiveness of microbial inoculation over N fertilization in promoting plant growth and provide valuable insights for the sustainable management of willow plantations at different stages of development.
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Affiliation(s)
- Qing Li
- Key Laboratory for Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yue He
- Key Laboratory for Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jian Feng
- Key Laboratory for Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yutong He
- Key Laboratory for Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Sheng Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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De la Vega-Camarillo E, Sotelo-Aguilar J, González-Silva A, Hernández-García JA, Mercado-Flores Y, Villa-Tanaca L, Hernández-Rodríguez C. Genomic Insights into Pseudomonas protegens E1BL2 from Giant Jala Maize: A Novel Bioresource for Sustainable Agriculture and Efficient Management of Fungal Phytopathogens. Int J Mol Sci 2024; 25:9508. [PMID: 39273455 PMCID: PMC11395412 DOI: 10.3390/ijms25179508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/23/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
The relationships between plants and bacteria are essential in agroecosystems and bioinoculant development. The leaf endophytic Pseudomonas protegens E1BL2 was previously isolated from giant Jala maize, which is a native Zea mays landrace of Nayarit, Mexico. Using different Mexican maize landraces, this work evaluated the strain's plant growth promotion and biocontrol against eight phytopathogenic fungi in vitro and greenhouse conditions. Also, a plant field trial was conducted on irrigated fields using the hybrid maize Supremo. The grain productivity in this assay increased compared with the control treatment. The genome analysis of P. protegens E1BL2 showed putative genes involved in metabolite synthesis that facilitated its beneficial roles in plant health and environmental adaptation (bdhA, acoR, trpE, speE, potA); siderophores (ptaA, pchC); and extracellular enzymes relevant for PGPB mechanisms (cel3, chi14), protection against oxidative stress (hscA, htpG), nitrogen metabolism (nirD, nit1, hmpA), inductors of plant-induced systemic resistance (ISR) (flaA, flaG, rffA, rfaP), fungal biocontrol (phlD, prtD, prnD, hcnA-1), pest control (vgrG-1, higB-2, aprE, pslA, ppkA), and the establishment of plant-bacteria symbiosis (pgaA, pgaB, pgaC, exbD). Our findings suggest that P. protegens E1BL2 significantly promotes maize growth and offers biocontrol benefits, which highlights its potential as a bioinoculant.
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Affiliation(s)
- Esaú De la Vega-Camarillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de México 11340, Mexico
| | - Josimar Sotelo-Aguilar
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de México 11340, Mexico
| | - Adilene González-Silva
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de México 11340, Mexico
| | - Juan Alfredo Hernández-García
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de México 11340, Mexico
| | - Yuridia Mercado-Flores
- Laboratorio de Aprovechamiento Integral de Recursos Bióticos, Universidad Politécnica de Pachuca, Carretera Pachuca-Ciudad Sahagún Km. 20, Rancho Luna, Ex-Hacienda de Santa Bárbara Zempoala, Pachuca 43830, Mexico
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de México 11340, Mexico
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de México 11340, Mexico
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Ambrosio R, Burgos Herrera G, Do Nascimento M, Pagnussat LA, Curatti L. Competitive fitness and stability of ammonium-excreting Azotobacter vinelandii strains in the soil. Appl Microbiol Biotechnol 2024; 108:378. [PMID: 38888816 PMCID: PMC11189346 DOI: 10.1007/s00253-024-13231-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/03/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
Non-symbiotic N2-fixation would greatly increase the versatility of N-biofertilizers for sustainable agriculture. Genetic modification of diazotrophic bacteria has successfully enhanced NH4+ release. In this study, we compared the competitive fitness of A. vinelandii mutant strains, which allowed us to analyze the burden of NH4+ release under a broad dynamic range. Long-term competition assays under regular culture conditions confirmed a large burden for NH4+ release, exclusion by the wt strain, phenotypic instability, and loss of the ability to release NH4+. In contrast, co-inoculation in mild autoclaved soil showed a much longer co-existence with the wt strain and a stable NH4+ release phenotype. All genetically modified strains increased the N content and changed its chemical speciation in the soil. This study contributes one step forward towards bridging a knowledge gap between molecular biology laboratory research and the incorporation of N from the air into the soil in a molecular species suitable for plant nutrition, a crucial requirement for developing improved bacterial inoculants for economic and environmentally sustainable agriculture. KEY POINTS: • Genetic engineering for NH4+ excretion imposes a fitness burden on the culture medium • Large phenotypic instability for NH4+-excreting bacteria in culture medium • Lower fitness burden and phenotypic instability for NH4+-excreting bacteria in soil.
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Affiliation(s)
- Rafael Ambrosio
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas, Vieytes 3103, 7600, Mar del PlataBuenos Aires, Argentina
- Fundación para Investigaciones Biológicas Aplicadas, Mar del Plata, Buenos Aires, Argentina
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Santa Fe, Santa Fe, Argentina
| | - Gonzalo Burgos Herrera
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas, Vieytes 3103, 7600, Mar del PlataBuenos Aires, Argentina
- Fundación para Investigaciones Biológicas Aplicadas, Mar del Plata, Buenos Aires, Argentina
| | - Mauro Do Nascimento
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas, Vieytes 3103, 7600, Mar del PlataBuenos Aires, Argentina
- Fundación para Investigaciones Biológicas Aplicadas, Mar del Plata, Buenos Aires, Argentina
| | - Luciana Anabella Pagnussat
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas, Vieytes 3103, 7600, Mar del PlataBuenos Aires, Argentina
- Fundación para Investigaciones Biológicas Aplicadas, Mar del Plata, Buenos Aires, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Buenos Aires, Argentina
| | - Leonardo Curatti
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas, Vieytes 3103, 7600, Mar del PlataBuenos Aires, Argentina.
- Fundación para Investigaciones Biológicas Aplicadas, Mar del Plata, Buenos Aires, Argentina.
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Alam M, Pandit B, Moin A, Iqbal UN. Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture. Indian J Microbiol 2024; 64:343-366. [PMID: 39011025 PMCID: PMC11246410 DOI: 10.1007/s12088-024-01225-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/07/2024] [Indexed: 07/17/2024] Open
Abstract
Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.
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Affiliation(s)
- Masrure Alam
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
| | - Baishali Pandit
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
- Department of Botany, Surendranath College, 24/2 MG Road, Kolkata, West Bengal 700009 India
| | - Abdul Moin
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
| | - Umaimah Nuzhat Iqbal
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
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Sun R, Zhu X, Wang C, Yue J, Pan L, Song C, Zhao Y. Effect of NH 4+ and NO 3- cooperatively regulated carbon to nitrogen ratio on organic nitrogen fractions during rice straw composting. BIORESOURCE TECHNOLOGY 2024; 395:130316. [PMID: 38218410 DOI: 10.1016/j.biortech.2024.130316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The purpose of this study was to examine the effects of replacing urea with inorganic nitrogen on the organic nitrogen sequestration process and the mitigation of nitrogen loss during rice straw composting. These groups include a control group with urea addition (CK), a group with (NH4)2SO4 addition (NH), a group with KNO3 addition (NO), and a group with (NH4)2SO4 + KNO3 addition (NN). The results demonstrated that adding NH, NO, and NN significantly increased the content of bioavailable organic nitrogen in the composting. Furthermore, compared to the CK, the NH treatment reduced nitrogen loss by 8.41 %. Structural equation modeling revealed the correlation between bacterial communities and organic nitrogen fractions in different treatment groups. Comparisons of nitrogen efficacy and nitrogen loss indicated that adding (NH4)2SO4 was more effective during composting, which provided a meaningful research basis for rice straw composting.
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Affiliation(s)
- Rui Sun
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xide Zhu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Chao Wang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jieyu Yue
- College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Lina Pan
- College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Caihong Song
- School of Life Science, Liaocheng University, Liaocheng 252000, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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Huang D, Ren J, Chen X, Akhtar K, Liang Q, Ye C, Xiong C, He H, He B. Whole-genome assembly of A02 bacteria involved in nitrogen fixation within cassava leaves. PLANT PHYSIOLOGY 2023; 193:1479-1490. [PMID: 37307568 DOI: 10.1093/plphys/kiad331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 06/14/2023]
Abstract
The endophytic nitrogen (N)-fixing bacterium A02 belongs to the genus Curtobacterium (Curtobacterium sp.) and is crucial for the N metabolism of cassava ( Manihot esculenta Crantz). We isolated the A02 strain from cassava cultivar SC205 and used the 15N isotope dilution method to study the impacts of A02 on growth and accumulation of N in cassava seedlings. Furthermore, the whole genome was sequenced to determine the N-fixation mechanism of A02. Compared with low N control (T1), inoculation with the A02 strain (T2) showed the highest increase in leaf and root dry weight of cassava seedlings, and 120.3 nmol/(mL·h) was the highest nitrogenase activity recorded in leaves, which were considered the main site for colonization and N-fixation. The genome of A02 was 3,555,568 bp in size and contained a circular chromosome and a plasmid. Comparison with the genomes of other short bacilli revealed that strain A02 showed evolutionary proximity to the endophytic bacterium NS330 (Curtobacterium citreum) isolated from rice (Oryza sativa) in India. The genome of A02 contained 13 nitrogen fixation (nif) genes, including 4 nifB, 1 nifR3, 2 nifH, 1 nifU, 1 nifD, 1 nifK, 1 nifE, 1 nifN, and 1 nifC, and formed a relatively complete N fixation gene cluster 8-kb long that accounted for 0.22% of the whole genome length. The nifHDK of strain A02 (Curtobacterium sp.) is identical to the Frankia alignment. Function prediction showed high copy number of the nifB gene was related to the oxygen protection mechanism. Our findings provide exciting information about the bacterial genome in relation to N support for transcriptomic and functional studies for increasing N use efficiency in cassava.
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Affiliation(s)
- Danping Huang
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, P. R. China
| | - Jie Ren
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, P. R. China
- Department of Agricultural Engineering, GuiZhou Vocational College of Agriculture, Qingzhen 550000, P. R. China
| | - Xi Chen
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, P. R. China
- Hunan Linji Ecological Technology Co. LtD., Hunan Province, Changsha 410000, P. R. China
| | - Kashif Akhtar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, P. R. China
| | - Qiongyue Liang
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, P. R. China
| | - Congyu Ye
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, P. R. China
| | - Caiyi Xiong
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, P. R. China
| | - Huahong He
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, P. R. China
| | - Bing He
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, P. R. China
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Sanow S, Kuang W, Schaaf G, Huesgen P, Schurr U, Roessner U, Watt M, Arsova B. Molecular Mechanisms of Pseudomonas-Assisted Plant Nitrogen Uptake: Opportunities for Modern Agriculture. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:536-548. [PMID: 36989040 DOI: 10.1094/mpmi-10-22-0223-cr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT, and Pseudomonas sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri, and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas-driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas-driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Stefan Sanow
- Institute for Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, Germany
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Weiqi Kuang
- College of life and Environmental Sciences, Hunan University of Arts and Science, China
| | - Gabriel Schaaf
- Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Pitter Huesgen
- Central institute for Engineering, Electronics and Analytics (ZEA-3), Forschungszentrum Juelich GmbH, Germany
| | - Ulrich Schurr
- Institute for Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, Germany
| | - Ute Roessner
- Research School of Biology, The Australian National University, Acton, 2601 Australian Capital Territory, Australia
| | - Michelle Watt
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Borjana Arsova
- Institute for Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, Germany
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Watanabe Y, Aoki W, Ueda M. Ammonia Production Using Bacteria and Yeast toward a Sustainable Society. Bioengineering (Basel) 2023; 10:82. [PMID: 36671654 PMCID: PMC9854848 DOI: 10.3390/bioengineering10010082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/29/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Ammonia is an important chemical that is widely used in fertilizer applications as well as in the steel, chemical, textile, and pharmaceutical industries, which has attracted attention as a potential fuel. Thus, approaches to achieve sustainable ammonia production have attracted considerable attention. In particular, biological approaches are important for achieving a sustainable society because they can produce ammonia under mild conditions with minimal environmental impact compared with chemical methods. For example, nitrogen fixation by nitrogenase in heterogeneous hosts and ammonia production from food waste using microorganisms have been developed. In addition, crop production using nitrogen-fixing bacteria has been considered as a potential approach to achieving a sustainable ammonia economy. This review describes previous research on biological ammonia production and provides insights into achieving a sustainable society.
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Affiliation(s)
- Yukio Watanabe
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Wataru Aoki
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8501, Japan
| | - Mitsuyoshi Ueda
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8501, Japan
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Bao YQ, Zhang MT, Feng BY, Jieensi W, Xu Y, Xu LR, Han YY, Chen YP. Construction, Characterization, and Application of an Ammonium Transporter (AmtB) Deletion Mutant of the Nitrogen-Fixing Bacterium Kosakonia radicincitans GXGL-4A in Cucumis sativus L. Seedlings. Curr Microbiol 2023; 80:58. [PMID: 36588112 DOI: 10.1007/s00284-022-03160-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 12/19/2022] [Indexed: 01/03/2023]
Abstract
Nitrogen is an important factor affecting crop yield, but excessive use of chemical nitrogen fertilizer has caused decline in nitrogen utilization and soil and water pollution. Reducing the utilization of chemical nitrogen fertilizers by biological nitrogen fixation (BNF) is feasible for green production of crops. However, there are few reports on how to have more ammonium produced by nitrogen-fixing bacteria (NFB) flow outside the cell. In the present study, the amtB gene encoding an ammonium transporter (AmtB) in the genome of NFB strain Kosakonia radicincitans GXGL-4A was deleted and the △amtB mutant was characterized. The results showed that deletion of the amtB gene had no influence on the growth of bacterial cells. The extracellular ammonium nitrogen (NH4+) content of the △amtB mutant under nitrogen-free culture conditions was significantly higher than that of the wild-type strain GXGL-4A (WT-GXGL-4A), suggesting disruption of NH4+ transport. Meanwhile, the plant growth-promoting effect in cucumber seedlings was visualized after fertilization using cells of the △amtB mutant. NFB fertilization continuously increased the cucumber rhizosphere soil pH. The nitrate nitrogen (NO3-) content in soil in the △amtB treatment group was significantly higher than that in the WT-GXGL-4A treatment group in the short term but there was no difference in soil NH4+ contents between groups. Soil enzymatic activities varied during a 45-day assessment period, indicating that △amtB fertilization influenced soil nitrogen cycling in the cucumber rhizosphere. The results will provide a solid foundation for developing the NFB GXGL-4A into an efficient biofertilizer agent.
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Affiliation(s)
- Yu-Qing Bao
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Meng-Ting Zhang
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bao-Yun Feng
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wulale Jieensi
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu Xu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Lu-Rong Xu
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ying-Ying Han
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Yun-Peng Chen
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Ministry of Science and Technology, Shanghai Yangtze River Delta Eco-Environmental Change and Research Station, Shanghai, 200240, China.
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Sarkar S, Kamke A, Ward K, Hartung E, Ran Q, Feehan B, Galliart M, Jumpponen A, Johnson L, Lee STM. Pseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience. BMC Genomics 2022; 23:784. [PMID: 36451103 PMCID: PMC9710129 DOI: 10.1186/s12864-022-09019-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Climate change will result in more frequent droughts that can impact soil-inhabiting microbiomes (rhizobiomes) in the agriculturally vital North American perennial grasslands. Rhizobiomes have contributed to enhancing drought resilience and stress resistance properties in plant hosts. In the predicted events of more future droughts, how the changing rhizobiome under environmental stress can impact the plant host resilience needs to be deciphered. There is also an urgent need to identify and recover candidate microorganisms along with their functions, involved in enhancing plant resilience, enabling the successful development of synthetic communities. RESULTS In this study, we used the combination of cultivation and high-resolution genomic sequencing of bacterial communities recovered from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified a bacterial genome of interest - MAG-Pseudomonas. Further metabolic pathway and pangenome analyses recovered genes and pathways related to stress responses including ACC deaminase; nitrogen transformation including assimilatory nitrate reductase in MAG-Pseudomonas, which might be associated with enhanced drought tolerance and growth for Andropogon gerardii. CONCLUSIONS Our data indicated that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host's growth during stressful conditions. Our study also suggested the nitrogen transformation potential of MAG-Pseudomonas that could impact Andropogon gerardii growth in a positive way. The cultivation of MAG-Pseudomonas sets the foundation to construct a successful synthetic community for Andropogon gerardii. To conclude, stress resilience mediated through genes ACC deaminase, nitrogen transformation potential through assimilatory nitrate reductase in MAG-Pseudomonas could place this microorganism as an important candidate of the rhizobiome aiding the plant host resilience under environmental stress. This study, therefore, provided insights into the MAG-Pseudomonas and its potential to optimize plant productivity under ever-changing climatic patterns, especially in frequent drought conditions.
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Affiliation(s)
- Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Abigail Kamke
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Kaitlyn Ward
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Eli Hartung
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Brandi Feehan
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Matthew Galliart
- Department of Biological Sciences, Fort Hays State University, Hays, KS, USA
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Loretta Johnson
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Sonny T M Lee
- Division of Biology, Kansas State University, Manhattan, KS, USA.
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11
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Wang M, Sun H, Xu Z. Analysis of Blueberry Plant Rhizosphere Bacterial Diversity and Selection of Plant Growth Promoting Rhizobacteria. Curr Microbiol 2022; 79:331. [DOI: 10.1007/s00284-022-03031-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/08/2022] [Indexed: 11/03/2022]
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12
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Baysal C, Burén S, He W, Jiang X, Capell T, Rubio LM, Christou P. Functional expression of the nitrogenase Fe protein in transgenic rice. Commun Biol 2022; 5:1006. [PMID: 36198910 PMCID: PMC9534833 DOI: 10.1038/s42003-022-03921-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Engineering cereals to express functional nitrogenase is a long-term goal of plant biotechnology and would permit partial or total replacement of synthetic N fertilizers by metabolization of atmospheric N2. Developing this technology is hindered by the genetic and biochemical complexity of nitrogenase biosynthesis. Nitrogenase and many of the accessory proteins involved in its assembly and function are O2 sensitive and only sparingly soluble in non-native hosts. We generated transgenic rice plants expressing the nitrogenase structural component, Fe protein (NifH), which carries a [4Fe-4S] cluster in its active form. NifH from Hydrogenobacter thermophilus was targeted to mitochondria together with the putative peptidyl prolyl cis-trans isomerase NifM from Azotobacter vinelandii to assist in NifH polypeptide folding. The isolated NifH was partially active in electron transfer to the MoFe protein nitrogenase component (NifDK) and in the biosynthesis of the nitrogenase iron-molybdenum cofactor (FeMo-co), two fundamental roles for NifH in N2 fixation. NifH functionality was, however, limited by poor [4Fe-4S] cluster occupancy, highlighting the importance of in vivo [Fe-S] cluster insertion and stability to achieve biological N2 fixation in planta. Nevertheless, the expression and activity of a nitrogenase component in rice plants represents the first major step to engineer functional nitrogenase in cereal crops.
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Affiliation(s)
- Can Baysal
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, 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), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Wenshu He
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Xi Jiang
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Teresa Capell
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, 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), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain.
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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Halotolerant rhizobacteria isolated from a mangrove forest alleviate saline stress in Musa acuminata cv. Berangan. Microbiol Res 2022; 265:127176. [PMID: 36088726 DOI: 10.1016/j.micres.2022.127176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 08/09/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022]
Abstract
Saline soils resulting from anthropogenic activity and climate change present a challenge to future food security. Towards addressing this, we isolated and characterized halotolerant bacteria from a Malaysian mangrove forest, and explored their effect on morpho-physiological and biochemical parameters of banana plantlets under salt stress. A total of 88 rhizobacterial and 16 endophytic bacterial isolates collected from the roots and rhizosphere of Rhizophora apiculata, Avicennia alba and Sonneratia alba, were found to tolerate up to 400 mM of sea salt. Based on best performance in multiple plant growth traits, three rhizobacterial strains RB1, RB3 and RB4 and three endophytic bacterial strains EB1, EB2 and EB3 were used for further analysis. The rhizobacterial strains were identified as Bacillus sp. and endophytic bacteria as Pseudomonas sp. based on 16 S rRNA gene sequence. SEM observation confirmed colonization of each strain on banana plantlet roots. When colonized plantlets were subjected to 90 mM salt and compared to uninoculated (control) and mock inoculated plants, improved plant growth was observed with each of the strains, especially with bacterial strains EB3 and RB3. Biochemical analysis of plantlets revealed that root colonization with EB3 and RB3 enhanced levels of plant chlorophyll (> 5-fold), carotenoid (> 2.85-fold) and proline (2.6-fold and 2.3-fold), while plantlets also showed reduced MDA content (0.45-fold and 0.51-fold), significantly reduced generation of ROS (0.23-fold and 0.47-fold) and lower levels of electrolyte leakage (0.77 and 0.51-fold). Antioxidant enzymes also showed enhanced activity with EB3 and RB3. Our results indicate that these halotolerant Bacillus and Pseudomonas strains from the mangrove have multifunctional plant growth promoting activity and can reduce salt stress in bananas. This data provides a reference for exploring halotolerant microbes from hypersaline environments to overcome salt stress in plants.
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14
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Schillaci M, Raio A, Sillo F, Zampieri E, Mahmood S, Anjum M, Khalid A, Centritto M. Pseudomonas and Curtobacterium Strains from Olive Rhizosphere Characterized and Evaluated for Plant Growth Promoting Traits. PLANTS (BASEL, SWITZERLAND) 2022; 11:2245. [PMID: 36079627 PMCID: PMC9460707 DOI: 10.3390/plants11172245] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/12/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Plant growth promoting (PGP) bacteria are known to enhance plant growth and protect them from environmental stresses through different pathways. The rhizosphere of perennial plants, including olive, may represent a relevant reservoir of PGP bacteria. Here, seven bacterial strains isolated from olive rhizosphere have been characterized taxonomically by 16S sequencing and biochemically, to evaluate their PGP potential. Most strains were identified as Pseudomonas or Bacillus spp., while the most promising ones belonged to genera Pseudomonas and Curtobacterium. Those strains have been tested for their capacity to grow under osmotic or salinity stress and to improve the germination and early development of Triticum durum subjected or not to those stresses. The selected strains had the ability to grow under severe stress, and a positive effect has been observed in non-stressed seedlings inoculated with one of the Pseudomonas strains, which showed promising characteristics that should be further evaluated. The biochemical and taxonomical characterization of bacterial strains isolated from different niches and the evaluation of their interaction with plants under varying conditions will help to increase our knowledge on PGP microorganisms and their use in agriculture.
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Affiliation(s)
- Martino Schillaci
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
| | - Aida Raio
- National Research Council, Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Fabiano Sillo
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
| | - Elisa Zampieri
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
| | - Shahid Mahmood
- Department of Environmental Sciences, PMAS Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Muzammil Anjum
- Department of Environmental Sciences, PMAS Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Azeem Khalid
- Department of Environmental Sciences, PMAS Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Mauro Centritto
- National Research Council, Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
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15
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Ladha JK, Peoples MB, Reddy PM, Biswas JC, Bennett A, Jat ML, Krupnik TJ. Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems. FIELD CROPS RESEARCH 2022; 283:108541. [PMID: 35782167 PMCID: PMC9133800 DOI: 10.1016/j.fcr.2022.108541] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 05/02/2023]
Abstract
The demand for nitrogen (N) for crop production increased rapidly from the middle of the twentieth century and is predicted to at least double by 2050 to satisfy the on-going improvements in productivity of major food crops such as wheat, rice and maize that underpin the staple diet of most of the world's population. The increased demand will need to be fulfilled by the two main sources of N supply - biological nitrogen (gas) (N2) fixation (BNF) and fertilizer N supplied through the Haber-Bosch processes. BNF provides many functional benefits for agroecosystems. It is a vital mechanism for replenishing the reservoirs of soil organic N and improving the availability of soil N to support crop growth while also assisting in efforts to lower negative environmental externalities than fertilizer N. In cereal-based cropping systems, legumes in symbiosis with rhizobia contribute the largest BNF input; however, diazotrophs involved in non-symbiotic associations with plants or present as free-living N2-fixers are ubiquitous and also provide an additional source of fixed N. This review presents the current knowledge of BNF by free-living, non-symbiotic and symbiotic diazotrophs in the global N cycle, examines global and regional estimates of contributions of BNF, and discusses possible strategies to enhance BNF for the prospective benefit of cereal N nutrition. We conclude by considering the challenges of introducing in planta BNF into cereals and reflect on the potential for BNF in both conventional and alternative crop management systems to encourage the ecological intensification of cereal and legume production.
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Affiliation(s)
- Jagdish K. Ladha
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mark B. Peoples
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | | | | | - Alan Bennett
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mangi L. Jat
- International Maize and Wheat Improvement Center, New Delhi, India
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16
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Bian Z, Wang M, Yang Y, Wu Y, Ni H, Yu X, Shi J, Chen H, Bian X, Pan D, Li T, Zhang Y, Yu L, Jiang L, Tu Q. Enhanced growth of ginger plants by an eco- friendly nitrogen-fixing Pseudomonas protegens inoculant in glasshouse fields. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3038-3046. [PMID: 34778957 PMCID: PMC9299100 DOI: 10.1002/jsfa.11645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/11/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Excessive nitrogen (N) fertilization in glasshouse fields greatly increases N loss and fossil-fuel energy consumption resulting in serious environmental risks. Microbial inoculants are strongly emerging as potential alternatives to agrochemicals and offer an eco-friendly fertilization strategy to reduce our dependence on synthetic chemical fertilizers. Effects of a N-fixing strain Pseudomonas protegens CHA0-ΔretS-nif on ginger plant growth, yield, and nutrient uptake, and on earthworm biomass and the microbial community were investigated in glasshouse fields in Shandong Province, northern China. RESULTS Application of CHA0-ΔretS-nif could promote ginger plant development, and significantly increased rhizome yields, by 12.93% and 7.09%, respectively, when compared to uninoculated plants and plants treated with the wild-type bacterial strain. Inoculation of CHA0-ΔretS-nif had little impact on plant phosphorus (P) acquisition, whereas it was associated with enhanced N and potassium (K) acquisition by ginger plants. Moreover, inoculation of CHA0-ΔretS-nif had positive effects on the bacteria population size and the number of earthworms in the rhizosphere. Similar enhanced performances were also found in CHA0-ΔretS-nif-inoculated ginger plants even when the N-fertilizer application rate was reduced by 15%. A chemical N input of 573.8 kg ha-1 with a ginger rhizome yield of 1.31 × 105 kg ha-1 was feasible. CONCLUSIONS The combined application of CHA0-ΔretS-nif and a reduced level of N-fertilizers can be employed in glasshouse ginger production for the purpose of achieving high yields while at the same time reducing the inorganic-N pollution from traditional farming practices. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Zhilong Bian
- Helmholtz International Laboratory for Anti‐Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Mei Wang
- Institute of Agricultural Resources and EnvironmentShandong Academy of Agricultural SciencesJinanChina
| | - Yan Yang
- Institute of Agricultural Resources and EnvironmentShandong Academy of Agricultural SciencesJinanChina
| | - Yuxia Wu
- Helmholtz International Laboratory for Anti‐Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Haiping Ni
- Helmholtz International Laboratory for Anti‐Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Xu Yu
- Institute of Agricultural Resources and EnvironmentShandong Academy of Agricultural SciencesJinanChina
| | - Jing Shi
- Institute of Agricultural Resources and EnvironmentShandong Academy of Agricultural SciencesJinanChina
| | - Hanna Chen
- Helmholtz International Laboratory for Anti‐Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Xiaoying Bian
- Helmholtz International Laboratory for Anti‐Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Deng Pan
- Helmholtz International Laboratory for Anti‐Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Tao Li
- Soil and Fertilizer Station of Shandong ProvinceShandong Provincial Department of AgricultureJinanChina
| | - Youming Zhang
- Helmholtz International Laboratory for Anti‐Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Lei Yu
- Soil and Fertilizer Station of Shandong ProvinceShandong Provincial Department of AgricultureJinanChina
| | - Lihua Jiang
- Institute of Agricultural Resources and EnvironmentShandong Academy of Agricultural SciencesJinanChina
| | - Qiang Tu
- Helmholtz International Laboratory for Anti‐Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
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17
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Shamseldin A. Future Outlook of Transferring Biological Nitrogen Fixation (BNF) to Cereals and Challenges to Retard Achieving this Dream. Curr Microbiol 2022; 79:171. [PMID: 35476236 DOI: 10.1007/s00284-022-02852-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 03/21/2022] [Indexed: 11/03/2022]
Abstract
BNF is a fascinating phenomenon which contributes to protect the nature from environmental pollution that can be happened as a result of heavy nitrogen applications. The importance of BNF is due to its supply of the agricultural lands with about 200 million tons of N annually. In this biological process, a specific group of bacteria collectively called rhizobia fix the atmospheric N in symbiosis with legumes called symbiotic nitrogen fixation and others (free living) fix nitrogen gas from the atmosphere termed asymbiotic. Several trials were done by scientists around the world to make cereals more benefited from nitrogen gas through different approaches. The first approach is to engineer cereals to form nodulated roots. Secondly is to transfer nif genes directly to cereals and fix N without Rhizobium partner. The other two approaches are maximizing the inoculation of cereals with both of diazotrophs or endophytes. Recently, scientists solved some challenges that entangle engineering cereals with nif genes directly and they confirmed the suitability of mitochondria and plastids as a suitable place for better biological function of nif genes expression in cereals. Fortunately, this article is confirming the success of scientists not only to transfer synthetic nitrogenase enzyme to Escherichia coli that gave 50% of its activity of expression, but also move it to plants as Nicotiana benthamiana. This mini review aims at explaining the future outlook of BNF and the challenges limiting its transfer to cereals and levels of success to make cereals self nitrogen fixing.
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Affiliation(s)
- Abdelaal Shamseldin
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, New Borg El Arab, Alexandria, Egypt.
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18
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Gruet C, Muller D, Moënne-Loccoz Y. Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome. Front Microbiol 2022; 12:782135. [PMID: 35058901 PMCID: PMC8764353 DOI: 10.3389/fmicb.2021.782135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.
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Affiliation(s)
| | | | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
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19
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Wen A, Havens KL, Bloch SE, Shah N, Higgins DA, Davis-Richardson AG, Sharon J, Rezaei F, Mohiti-Asli M, Johnson A, Abud G, Ane JM, Maeda J, Infante V, Gottlieb SS, Lorigan JG, Williams L, Horton A, McKellar M, Soriano D, Caron Z, Elzinga H, Graham A, Clark R, Mak SM, Stupin L, Robinson A, Hubbard N, Broglie R, Tamsir A, Temme K. Enabling Biological Nitrogen Fixation for Cereal Crops in Fertilized Fields. ACS Synth Biol 2021; 10:3264-3277. [PMID: 34851109 DOI: 10.1021/acssynbio.1c00049] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Agricultural productivity relies on synthetic nitrogen fertilizers, yet half of that reactive nitrogen is lost to the environment. There is an urgent need for alternative nitrogen solutions to reduce the water pollution, ozone depletion, atmospheric particulate formation, and global greenhouse gas emissions associated with synthetic nitrogen fertilizer use. One such solution is biological nitrogen fixation (BNF), a component of the complex natural nitrogen cycle. BNF application to commercial agriculture is currently limited by fertilizer use and plant type. This paper describes the identification, development, and deployment of the first microbial product optimized using synthetic biology tools to enable BNF for corn (Zea mays) in fertilized fields, demonstrating the successful, safe commercialization of root-associated diazotrophs and realizing the potential of BNF to replace and reduce synthetic nitrogen fertilizer use in production agriculture. Derived from a wild nitrogen-fixing microbe isolated from agricultural soils, Klebsiella variicola 137-1036 ("Kv137-1036") retains the capacity of the parent strain to colonize corn roots while increasing nitrogen fixation activity 122-fold in nitrogen-rich environments. This technical milestone was then commercialized in less than half of the time of a traditional biological product, with robust biosafety evaluations and product formulations contributing to consumer confidence and ease of use. Tested in multi-year, multi-site field trial experiments throughout the U.S. Corn Belt, fields grown with Kv137-1036 exhibited both higher yields (0.35 ± 0.092 t/ha ± SE or 5.2 ± 1.4 bushels/acre ± SE) and reduced within-field yield variance by 25% in 2018 and 8% in 2019 compared to fields fertilized with synthetic nitrogen fertilizers alone. These results demonstrate the capacity of a broad-acre BNF product to fix nitrogen for corn in field conditions with reliable agronomic benefits.
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Affiliation(s)
- Amy Wen
- Pivot Bio, Berkeley, California 94710, United States
| | | | - Sarah E. Bloch
- Morrison & Foerster LLP, San Francisco, California 94105, United States
| | - Neal Shah
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | - Judee Sharon
- University of Minnesota─Twin Cities, Minneapolis, Minnesota 55401, United States
| | | | | | | | - Gabriel Abud
- Tempo Automation, San Francisco, California 94103, United States
| | - Jean-Michel Ane
- University of Minnesota─Twin Cities, Minneapolis, Minnesota 55401, United States
| | - Junko Maeda
- University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Valentina Infante
- University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | | | | | | | - Alana Horton
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | - Zoe Caron
- Pivot Bio, Berkeley, California 94710, United States
| | | | - Ashley Graham
- Olema Oncology, San Francisco, California 94107, United States
| | | | - San-Ming Mak
- Pivot Bio, Berkeley, California 94710, United States
| | - Laura Stupin
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | | | - Alvin Tamsir
- Pivot Bio, Berkeley, California 94710, United States
| | - Karsten Temme
- Pivot Bio, Berkeley, California 94710, United States
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Schnabel T, Sattely E. Improved Stability of Engineered Ammonia Production in the Plant-Symbiont Azospirillum brasilense. ACS Synth Biol 2021; 10:2982-2996. [PMID: 34591447 PMCID: PMC8604774 DOI: 10.1021/acssynbio.1c00287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioavailable nitrogen is the limiting nutrient for most agricultural food production. Associative diazotrophs can colonize crop roots and fix their own bioavailable nitrogen from the atmosphere. Wild-type (WT) associative diazotrophs, however, do not release fixed nitrogen in culture and are not known to directly transfer fixed nitrogen resources to plants. Efforts to engineer diazotrophs for plant nitrogen provision as an alternative to chemical fertilization have yielded several strains that transiently release ammonia. However, these strains suffer from selection pressure for nonproducers, which rapidly deplete ammonia accumulating in culture, likely limiting their potential for plant growth promotion (PGP). Here we report engineered Azospirillum brasilense strains with significantly extend ammonia production lifetimes of up to 32 days in culture. Our approach relies on multicopy genetic redundancy of a unidirectional adenylyltransferase (uAT) as a posttranslational mechanism to induce ammonia release via glutamine synthetase deactivation. Testing our multicopy stable strains with the model monocot Setaria viridis in hydroponic monoassociation reveals improvement in plant growth promotion compared to single copy strains. In contrast, inoculation of Zea mays in nitrogen-poor, nonsterile soil does not lead to increased PGP relative to WT, suggesting strain health, resource competition, or colonization capacity in soil may also be limiting factors. In this context, we show that while engineered strains fix more nitrogen per cell compared to WT strains, the expression strength of multiple uAT copies needs to be carefully balanced to maximize ammonia production rates and avoid excessive fitness defects caused by excessive glutamine synthetase shutdown.
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Affiliation(s)
- Tim Schnabel
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Elizabeth Sattely
- Department of Chemical Engineering, Stanford University and HHMI, Stanford, California 94305, United States
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21
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Korshunova TY, Bakaeva MD, Kuzina EV, Rafikova GF, Chetverikov SP, Chetverikova DV, Loginov ON. Role of Bacteria of the Genus Pseudomonas in the Sustainable Development of Agricultural Systems and Environmental Protection (Review). APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s000368382103008x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Udvardi M, Below FE, Castellano MJ, Eagle AJ, Giller KE, Ladha JK, Liu X, Maaz TM, Nova-Franco B, Raghuram N, Robertson GP, Roy S, Saha M, Schmidt S, Tegeder M, York LM, Peters JW. A Research Road Map for Responsible Use of Agricultural Nitrogen. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.660155] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nitrogen (N) is an essential but generally limiting nutrient for biological systems. Development of the Haber-Bosch industrial process for ammonia synthesis helped to relieve N limitation of agricultural production, fueling the Green Revolution and reducing hunger. However, the massive use of industrial N fertilizer has doubled the N moving through the global N cycle with dramatic environmental consequences that threaten planetary health. Thus, there is an urgent need to reduce losses of reactive N from agriculture, while ensuring sufficient N inputs for food security. Here we review current knowledge related to N use efficiency (NUE) in agriculture and identify research opportunities in the areas of agronomy, plant breeding, biological N fixation (BNF), soil N cycling, and modeling to achieve responsible, sustainable use of N in agriculture. Amongst these opportunities, improved agricultural practices that synchronize crop N demand with soil N availability are low-hanging fruit. Crop breeding that targets root and shoot physiological processes will likely increase N uptake and utilization of soil N, while breeding for BNF effectiveness in legumes will enhance overall system NUE. Likewise, engineering of novel N-fixing symbioses in non-legumes could reduce the need for chemical fertilizers in agroecosystems but is a much longer-term goal. The use of simulation modeling to conceptualize the complex, interwoven processes that affect agroecosystem NUE, along with multi-objective optimization, will also accelerate NUE gains.
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23
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Pankievicz VCS, do Amaral FP, Ané JM, Stacey G. Diazotrophic Bacteria and Their Mechanisms to Interact and Benefit Cereals. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:491-498. [PMID: 33543986 DOI: 10.1094/mpmi-11-20-0316-fi] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant-growth-promoting bacteria (PGPB) stimulate plant growth through diverse mechanisms. In addition to biological nitrogen fixation, diazotrophic PGPB can improve nutrient uptake efficiency from the soil, produce and release phytohormones to the host, and confer resistance against pathogens. The genetic determinants that drive the success of biological nitrogen fixation in nonlegume plants are understudied. These determinants include recognition and signaling pathways, bacterial colonization, and genotype specificity between host and bacteria. This review presents recent discoveries of how nitrogen-fixing PGPB interact with cereals and promote plant growth. We suggest adopting an experimental model system, such as the Setaria-diazotrophic bacteria association, as a reliable way to better understand the associated mechanisms and, ultimately, increase the use of PGPB inoculants for sustainable agriculture.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
| | - Fernanda Plucani do Amaral
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, U.S.A
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, U.S.A
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Haskett TL, Tkacz A, Poole PS. Engineering rhizobacteria for sustainable agriculture. THE ISME JOURNAL 2021; 15:949-964. [PMID: 33230265 PMCID: PMC8114929 DOI: 10.1038/s41396-020-00835-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023]
Abstract
Exploitation of plant growth promoting (PGP) rhizobacteria (PGPR) as crop inoculants could propel sustainable intensification of agriculture to feed our rapidly growing population. However, field performance of PGPR is typically inconsistent due to suboptimal rhizosphere colonisation and persistence in foreign soils, promiscuous host-specificity, and in some cases, the existence of undesirable genetic regulation that has evolved to repress PGP traits. While the genetics underlying these problems remain largely unresolved, molecular mechanisms of PGP have been elucidated in rigorous detail. Engineering and subsequent transfer of PGP traits into selected efficacious rhizobacterial isolates or entire bacterial rhizosphere communities now offers a powerful strategy to generate improved PGPR that are tailored for agricultural use. Through harnessing of synthetic plant-to-bacteria signalling, attempts are currently underway to establish exclusive coupling of plant-bacteria interactions in the field, which will be crucial to optimise efficacy and establish biocontainment of engineered PGPR. This review explores the many ecological and biotechnical facets of this research.
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Affiliation(s)
- Timothy L. Haskett
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Andrzej Tkacz
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Philip S. Poole
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
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Deferred control of ammonium cross-feeding in a N 2-fixing bacterium-microalga artificial consortium. Appl Microbiol Biotechnol 2021; 105:2937-2950. [PMID: 33687504 DOI: 10.1007/s00253-021-11210-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/22/2021] [Accepted: 02/28/2021] [Indexed: 10/22/2022]
Abstract
There is an increasing interest in the use of N2-fixing bacteria for the sustainable biofertilization of crops. Genetically-optimized bacteria for ammonium release have an improved biofertilization capacity. Some of these strains also cross-feed ammonium into microalgae raising additional concerns on their sustainable use in agriculture due to the potential risk of producing a higher and longer-lasting eutrophication problem than synthetic N-fertilizers. Here we studied the dynamic algal cross-feeding properties of a genetically-modified Azotobacter vinelandii strain which can be tuned to over-accumulate different levels of glutamine synthetase (GS, EC 6.3.1.20) under the control of an exogenous inducer. After switching cells overaccumulating GS into a noninducing medium, they proliferated for several generations at the expense of the previously accumulated GS. Further dilution of GS by cell division slowed-down growth, promoted ammonium-excretion and cross-fed algae. The final bacterial population, and timing and magnitude of algal N-biofertlization was finely tuned in a deferred manner. This tuning was in accordance with the intensity of the previous induction of GS accumulation in the cells. This bacterial population behavior could be maintained up to about 15 bacterial cell generations, until faster-growing and nonammonium excreting cells arose at an apparent high frequency. Further improvements of this genetic engineering strategy might help to align efficiency of N-biofertilizers and safe use in an open environment. KEY POINTS: • Ammonium-excreting bacteria are potential eutrophication agents • GS-dependent deferred control of bacterial growth and ammonium release • Strong but transient ammonium cross-feeding of microalgae.
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Brooks SM, Alper HS. Applications, challenges, and needs for employing synthetic biology beyond the lab. Nat Commun 2021; 12:1390. [PMID: 33654085 PMCID: PMC7925609 DOI: 10.1038/s41467-021-21740-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
Synthetic biology holds great promise for addressing global needs. However, most current developments are not immediately translatable to 'outside-the-lab' scenarios that differ from controlled laboratory settings. Challenges include enabling long-term storage stability as well as operating in resource-limited and off-the-grid scenarios using autonomous function. Here we analyze recent advances in developing synthetic biological platforms for outside-the-lab scenarios with a focus on three major application spaces: bioproduction, biosensing, and closed-loop therapeutic and probiotic delivery. Across the Perspective, we highlight recent advances, areas for further development, possibilities for future applications, and the needs for innovation at the interface of other disciplines.
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Affiliation(s)
- Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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27
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Goyal RK, Schmidt MA, Hynes MF. Molecular Biology in the Improvement of Biological Nitrogen Fixation by Rhizobia and Extending the Scope to Cereals. Microorganisms 2021; 9:microorganisms9010125. [PMID: 33430332 PMCID: PMC7825764 DOI: 10.3390/microorganisms9010125] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022] Open
Abstract
The contribution of biological nitrogen fixation to the total N requirement of food and feed crops diminished in importance with the advent of synthetic N fertilizers, which fueled the “green revolution”. Despite being environmentally unfriendly, the synthetic versions gained prominence primarily due to their low cost, and the fact that most important staple crops never evolved symbiotic associations with bacteria. In the recent past, advances in our knowledge of symbiosis and nitrogen fixation and the development and application of recombinant DNA technology have created opportunities that could help increase the share of symbiotically-driven nitrogen in global consumption. With the availability of molecular biology tools, rapid improvements in symbiotic characteristics of rhizobial strains became possible. Further, the technology allowed probing the possibility of establishing a symbiotic dialogue between rhizobia and cereals. Because the evolutionary process did not forge a symbiotic relationship with the latter, the potential of molecular manipulations has been tested to incorporate a functional mechanism of nitrogen reduction independent of microbes. In this review, we discuss various strategies applied to improve rhizobial strains for higher nitrogen fixation efficiency, more competitiveness and enhanced fitness under unfavorable environments. The challenges and progress made towards nitrogen self-sufficiency of cereals are also reviewed. An approach to integrate the genetically modified elite rhizobia strains in crop production systems is highlighted.
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Affiliation(s)
- Ravinder K. Goyal
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB T4L 1W1, Canada;
- Correspondence:
| | - Maria Augusta Schmidt
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB T4L 1W1, Canada;
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada;
| | - Michael F. Hynes
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada;
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28
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Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage. PLoS One 2020; 15:e0239677. [PMID: 32986754 PMCID: PMC7521700 DOI: 10.1371/journal.pone.0239677] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/11/2020] [Indexed: 01/22/2023] Open
Abstract
A geographically isolated maize landrace cultivated on nitrogen-depleted fields without synthetic fertilizer in the Sierra Mixe region of Oaxaca, Mexico utilizes nitrogen derived from the atmosphere and develops an extensive network of mucilage-secreting aerial roots that harbors a diazotrophic (N2-fixing) microbiota. Targeting these diazotrophs, we selected nearly 600 microbes of a collection obtained from mucilage and confirmed their ability to incorporate heavy nitrogen (15N2) metabolites in vitro. Sequencing their genomes and conducting comparative bioinformatic analyses showed that these genomes had substantial phylogenetic diversity. We examined each diazotroph genome for the presence of nif genes essential to nitrogen fixation (nifHDKENB) and carbohydrate utilization genes relevant to the mucilage polysaccharide digestion. These analyses identified diazotrophs that possessed the canonical nif gene operons, as well as many other operon configurations with concomitant fixation and release of >700 different 15N labeled metabolites. We further demonstrated that many diazotrophs possessed alternative nif gene operons and confirmed their genomic potential to derive chemical energy from mucilage polysaccharide to fuel nitrogen fixation. These results confirm that some diazotrophic bacteria associated with Sierra Mixe maize were capable of incorporating atmospheric nitrogen into their small molecule extracellular metabolites through multiple nif gene configurations while others were able to fix nitrogen without the canonical (nifHDKENB) genes.
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29
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Marmont LS, Whitfield GB, Pfoh R, Williams RJ, Randall TE, Ostaszewski A, Razvi E, Groves RA, Robinson H, Nitz M, Parsek MR, Lewis IA, Whitney JC, Harrison JJ, Howell PL. PelX is a UDP- N-acetylglucosamine C4-epimerase involved in Pel polysaccharide-dependent biofilm formation. J Biol Chem 2020; 295:11949-11962. [PMID: 32601062 PMCID: PMC7443510 DOI: 10.1074/jbc.ra120.014555] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/24/2020] [Indexed: 12/15/2022] Open
Abstract
Pel is a GalNAc-rich bacterial polysaccharide that contributes to the structure and function of Pseudomonas aeruginosa biofilms. The pelABCDEFG operon is highly conserved among diverse bacterial species, and Pel may therefore be a widespread biofilm determinant. Previous annotation of pel gene clusters has helped us identify an additional gene, pelX, that is present adjacent to pelABCDEFG in >100 different bacterial species. The pelX gene is predicted to encode a member of the short-chain dehydrogenase/reductase (SDR) superfamily, but its potential role in Pel-dependent biofilm formation is unknown. Herein, we have used Pseudomonas protegens Pf-5 as a model to elucidate PelX function as Pseudomonas aeruginosa lacks a pelX homologue in its pel gene cluster. We found that P. protegens forms Pel-dependent biofilms; however, despite expression of pelX under these conditions, biofilm formation was unaffected in a ΔpelX strain. This observation led us to identify a pelX paralogue, PFL_5533, which we designate here PgnE, that appears to be functionally redundant to pelX In line with this, a ΔpelX ΔpgnE double mutant was substantially impaired in its ability to form Pel-dependent biofilms. To understand the molecular basis for this observation, we determined the structure of PelX to 2.1 Å resolution. The structure revealed that PelX resembles UDP-GlcNAc C4-epimerases. Using 1H NMR analysis, we show that PelX catalyzes the epimerization between UDP-GlcNAc and UDP-GalNAc. Our results indicate that Pel-dependent biofilm formation requires a UDP-GlcNAc C4-epimerase that generates the UDP-GalNAc precursors required by the Pel synthase machinery for polymer production.
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Affiliation(s)
- Lindsey S Marmont
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Gregory B Whitfield
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Roland Pfoh
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rohan J Williams
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Trevor E Randall
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | | | - Erum Razvi
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ryan A Groves
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Howard Robinson
- Photon Science Division, Brookhaven National Laboratory, Upton, New York, USA
| | - Mark Nitz
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - John C Whitney
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Joe J Harrison
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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Bloch SE, Clark R, Gottlieb SS, Wood LK, Shah N, Mak SM, Lorigan JG, Johnson J, Davis-Richardson AG, Williams L, McKellar M, Soriano D, Petersen M, Horton A, Smith O, Wu L, Tung E, Broglie R, Tamsir A, Temme K. Biological nitrogen fixation in maize: optimizing nitrogenase expression in a root-associated diazotroph. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4591-4603. [PMID: 32267497 PMCID: PMC7382387 DOI: 10.1093/jxb/eraa176] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/09/2020] [Indexed: 05/04/2023]
Abstract
Plants depend upon beneficial interactions between roots and root-associated microorganisms for growth promotion, disease suppression, and nutrient availability. This includes the ability of free-living diazotrophic bacteria to supply nitrogen, an ecological role that has been long underappreciated in modern agriculture for efficient crop production systems. Long-term ecological studies in legume-rhizobia interactions have shown that elevated nitrogen inputs can lead to the evolution of less cooperative nitrogen-fixing mutualists. Here we describe how reprogramming the genetic regulation of nitrogen fixation and assimilation in a novel root-associated diazotroph can restore ammonium production in the presence of exogenous nitrogen inputs. We isolated a strain of the plant-associated proteobacterium Kosakonia sacchari from corn roots, characterized its nitrogen regulatory network, and targeted key nodes for gene editing to optimize nitrogen fixation in corn. While the wild-type strain exhibits repression of nitrogen fixation in conditions replete with bioavailable nitrogen, such as fertilized greenhouse and field experiments, remodeled strains show elevated levels in the rhizosphere of corn in the greenhouse and field even in the presence of exogenous nitrogen. Such strains could be used in commercial applications to supply fixed nitrogen to cereal crops.
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31
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Castro Tapia MP, Madariaga Burrows RP, Ruiz Sepúlveda B, Vargas Concha M, Vera Palma C, Moya-Elizondo EA. Antagonistic Activity of Chilean Strains of Pseudomonas protegens Against Fungi Causing Crown and Root Rot of Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2020; 11:951. [PMID: 32670339 PMCID: PMC7330486 DOI: 10.3389/fpls.2020.00951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Seed treatments with antagonistic bacteria could reduce the severity of crown and root rot diseases in wheat crops. The objective of this study was to evaluate the potential antagonistic activity of a bacterial consortium of three Chilean strains of Pseudomonas protegens against the wheat crown and root rot pathogens Gaeumannomyces graminis var. tritici, Rhizoctonia cerealis, and Fusarium culmorum. Two field experiments were carried out on artificially infested soil during two consecutive seasons (2016-2017 and 2017-2018) in an Andisol soil of southern Chile. Control treatments (not inoculated with fungi) were also included. Each treatment included a seed treatment of spring wheat cv. Pantera-INIA with and without the bacterial consortium. Both phytosanitary damage (incidence and severity) and agronomic components were evaluated. Bacterial populations with the phlD+ gene in the wheat plant rhizosphere during anthesis state (Z6) were also quantified. In both seasons, infection severity decreased by an average of 16.8% in seeds treated with P. protegens consortium, while yield components such as spikes m-1 and number of grains per spike increased. The use of antagonistic bacteria resulted in a total yield increase only during the first experimental season (P < 0.05). In general, accumulated rainfall influenced the antagonistic effect of the consortium of P. protegens strains, accounting for the differences observed between the two seasons. The results suggest that this P. protegens consortium applied on seeds can promote plant growth and protect wheat crops against crown and root rot pathogens in Southern Chile under field conditions.
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Affiliation(s)
- María Paz Castro Tapia
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile
| | | | - Braulio Ruiz Sepúlveda
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile
| | - Marisol Vargas Concha
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile
| | - Carola Vera Palma
- National Agricultural Research Institute, INIA Quilamapu, Chillán, Chile
| | - Ernesto A. Moya-Elizondo
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile
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32
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Qu Q, Zhang Z, Peijnenburg WJGM, Liu W, Lu T, Hu B, Chen J, Chen J, Lin Z, Qian H. Rhizosphere Microbiome Assembly and Its Impact on Plant Growth. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5024-5038. [PMID: 32255613 DOI: 10.1021/acs.jafc.0c00073] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Microorganisms colonizing the plant rhizosphere provide a number of beneficial functions for their host. Although an increasing number of investigations clarified the great functional capabilities of rhizosphere microbial communities, the understanding of the precise mechanisms underlying the impact of rhizosphere microbiome assemblies is still limited. Also, not much is known about the various beneficial functions of the rhizosphere microbiome. In this review, we summarize the current knowledge of biotic and abiotic factors that shape the rhizosphere microbiome as well as the rhizosphere microbiome traits that are beneficial to plants growth and disease-resistance. We give particular emphasis on the impact of plant root metabolites on rhizosphere microbiome assemblies and on how the microbiome contributes to plant growth, yield, and disease-resistance. Finally, we introduce a new perspective and a novel method showing how a synthetic microbial community construction provides an effective approach to unravel the plant-microbes and microbes-microbes interplays.
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Affiliation(s)
- Qian Qu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA Leiden, The Netherlands
- National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, 3720BA Bilthoven, The Netherlands
| | - Wanyue Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, P.R. China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, P.R. China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
| | - Jun Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
| | - Zhifen Lin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, P.R. China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.R. China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, P.R. China
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Bloch SE, Ryu MH, Ozaydin B, Broglie R. Harnessing atmospheric nitrogen for cereal crop production. Curr Opin Biotechnol 2020; 62:181-188. [DOI: 10.1016/j.copbio.2019.09.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/16/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022]
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34
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Ryu MH, Zhang J, Toth T, Khokhani D, Geddes BA, Mus F, Garcia-Costas A, Peters JW, Poole PS, Ané JM, Voigt CA. Control of nitrogen fixation in bacteria that associate with cereals. Nat Microbiol 2019; 5:314-330. [DOI: 10.1038/s41564-019-0631-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
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35
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Pankievicz VCS, Irving TB, Maia LGS, Ané JM. Are we there yet? The long walk towards the development of efficient symbiotic associations between nitrogen-fixing bacteria and non-leguminous crops. BMC Biol 2019; 17:99. [PMID: 31796086 PMCID: PMC6889567 DOI: 10.1186/s12915-019-0710-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 10/18/2019] [Indexed: 01/09/2023] Open
Abstract
Nitrogen is an essential element of life, and nitrogen availability often limits crop yields. Since the Green Revolution, massive amounts of synthetic nitrogen fertilizers have been produced from atmospheric nitrogen and natural gas, threatening the sustainability of global food production and degrading the environment. There is a need for alternative means of bringing nitrogen to crops, and taking greater advantage of biological nitrogen fixation seems a logical option. Legumes are used in most cropping systems around the world because of the nitrogen-fixing symbiosis with rhizobia. However, the world's three major cereal crops-rice, wheat, and maize-do not associate with rhizobia. In this review, we will survey how genetic approaches in rhizobia and their legume hosts allowed tremendous progress in understanding the molecular mechanisms controlling root nodule symbioses, and how this knowledge paves the way for engineering such associations in non-legume crops. We will also discuss challenges in bringing these systems into the field and how they can be surmounted by interdisciplinary collaborations between synthetic biologists, microbiologists, plant biologists, breeders, agronomists, and policymakers.
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Affiliation(s)
| | - Thomas B Irving
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Lucas G S Maia
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA.
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Andreozzi A, Prieto P, Mercado-Blanco J, Monaco S, Zampieri E, Romano S, Valè G, Defez R, Bianco C. Efficient colonization of the endophytes Herbaspirillum huttiense RCA24 and Enterobacter cloacae RCA25 influences the physiological parameters of Oryza sativa L. cv. Baldo rice. Environ Microbiol 2019; 21:3489-3504. [PMID: 31106946 DOI: 10.1111/1462-2920.14688] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 11/26/2022]
Abstract
Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilization, 1-aminocyclopropane-1-carboxylate deaminase activity and production of siderophores and phytohormones, can be assessed as plant growth promotion traits. Our aim was to evaluate the effects of nitrogen fixing and indole-3-acetic acid (IAA) producing endophytes in two Oryza sativa cultivars (Baldo and Vialone Nano). Three bacteria, Herbaspirillum huttiense RCA24, Enterobacter asburiae RCA23 and Staphylococcus sp. 377, producing different IAA levels, were tested for their ability to enhance nifH gene expression and nitrogenase activity in Enterobacter cloacae RCA25. Results showed that H. huttiense RCA24 performed best. Improvement in nitrogen fixation and changes in physiological parameters such as chlorophyll, nitrogen content and shoot dry weight were observed for plants co-inoculated with strains RCA25 and RCA24 in a 10:1 ratio. Based on confocal laser scanning microscopy analysis, strain RCA24 was the best colonizer of the root interior and the only IAA producer located in the same root niche occupied by RCA25 cells. This work shows that the choice of a bio-inoculum having the right composition is one of the key aspects to be considered for the inoculation of a specific host plant cultivar with microbial consortia.
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Affiliation(s)
- Anna Andreozzi
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Pilar Prieto
- Departamento de Mejora Genética, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus 'Alameda del Obispo', Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus 'Alameda del Obispo', Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Stefano Monaco
- CREA - CI, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy
| | - Elisa Zampieri
- CREA - CI, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy
| | - Silvia Romano
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Gianpiero Valè
- DiSIT, Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Piazza San Eusebio 5, I-13100 Vercelli, Italy
| | - Roberto Defez
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Carmen Bianco
- Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
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Geddes BA, Paramasivan P, Joffrin A, Thompson AL, Christensen K, Jorrin B, Brett P, Conway SJ, Oldroyd GED, Poole PS. Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria. Nat Commun 2019; 10:3430. [PMID: 31366919 PMCID: PMC6668481 DOI: 10.1038/s41467-019-10882-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 06/07/2019] [Indexed: 01/10/2023] Open
Abstract
The root microbiota is critical for agricultural yield, with growth-promoting bacteria able to solubilise phosphate, produce plant growth hormones, antagonise pathogens and fix N2. Plants control the microorganisms in their immediate environment and this is at least in part through direct selection, the immune system, and interactions with other microorganisms. Considering the importance of the root microbiota for crop yields it is attractive to artificially regulate this environment to optimise agricultural productivity. Towards this aim we express a synthetic pathway for the production of the rhizopine scyllo-inosamine in plants. We demonstrate the production of this bacterial derived signal in both Medicago truncatula and barley and show its perception by rhizosphere bacteria, containing bioluminescent and fluorescent biosensors. This study lays the groundwork for synthetic signalling networks between plants and bacteria, allowing the targeted regulation of bacterial gene expression in the rhizosphere for delivery of useful functions to plants. The root microbiota is critical for promoting crop yield. Here, the authors create a synthetic pathway for the production of the rhizopine scyllo-inosamine in Medicago truncatula and barley, and show its perception by rhizosphere bacteria for targeted regulation of bacterial gene expression.
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Affiliation(s)
- Barney A Geddes
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ponraj Paramasivan
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Amelie Joffrin
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Amber L Thompson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Kirsten Christensen
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Paul Brett
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Stuart J Conway
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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Burén S, Rubio LM. State of the art in eukaryotic nitrogenase engineering. FEMS Microbiol Lett 2019; 365:4733273. [PMID: 29240940 PMCID: PMC5812491 DOI: 10.1093/femsle/fnx274] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/11/2017] [Indexed: 12/27/2022] Open
Abstract
Improving the ability of plants and plant-associated organisms to fix and assimilate atmospheric nitrogen has inspired plant biotechnologists for decades, not only to alleviate negative effects on nature from increased use and availability of reactive nitrogen, but also because of apparent economic benefits and opportunities. The combination of recent advances in synthetic biology and increased knowledge about the biochemistry and biosynthesis of the nitrogenase enzyme has made the seemingly remote and for long unreachable dream more possible. In this review, we will discuss strategies how this could be accomplished using biotechnology, with a special focus on recent progress on engineering plants to express its own nitrogenase.
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Affiliation(s)
- Stefan Burén
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
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Seasonal Physiological Parameters and Phytotelmata Bacterial Diversity of Two Bromeliad Species (Aechmea gamosepala and Vriesea platynema) from the Atlantic Forest of Southern Brazil. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11070111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ecology of complex microhabitats remains poorly characterized in most tropical and subtropical biomes, and holds potential to help understand the structure and dynamics of different biodiversity components in these ecosystems. We assessed nutritional and metabolic parameters of two bromeliad species (Aechmea gamosepala and Vriesea platynema) at an Atlantic Forest site and used 16S rDNA metabarcoding to survey the microbial communities inhabiting their tanks. We observed that levels of some nutrients (e.g., nitrogen) varied across seasons consistently in both species, while others (e.g., phenolic compounds) presented considerable differences between the two bromeliads. In contrast, patterns of tank microbial diversity did not follow a similar temporal trend. There was extensive variation in microbial composition among samples, which included intra-specific differences but also some consistent differences between the two bromeliads. For example, Citrobacter, Klebsiella and Pantoea presented significantly different abundances in the two species. Interestingly, the dominant bacterial genera in both species included Pseudomonas and Enterobacter, which have been reported to include plant-beneficial species. Overall, our data contribute to the characterization of the nutritional status of Atlantic Forest bromeliads and the composition of their prokaryotic communities, laying the foundation for detailed investigations targeting the ecological interactions between these plants and their associated microbes.
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40
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Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit. Biochem Soc Trans 2019; 47:603-614. [PMID: 30936245 PMCID: PMC6490700 DOI: 10.1042/bst20180342] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 11/29/2022]
Abstract
Biological nitrogen fixation (BNF) is controlled by intricate regulatory mechanisms to ensure that fixed nitrogen is readily assimilated into biomass and not released to the environment. Understanding the complex regulatory circuits that couple nitrogen fixation to ammonium assimilation is a prerequisite for engineering diazotrophic strains that can potentially supply fixed nitrogen to non-legume crops. In this review, we explore how the current knowledge of nitrogen metabolism and BNF regulation may allow strategies for genetic manipulation of diazotrophs for ammonia excretion and provide a contribution towards solving the nitrogen crisis.
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41
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Pseudomonas protegens MP12: A plant growth-promoting endophytic bacterium with broad-spectrum antifungal activity against grapevine phytopathogens. Microbiol Res 2019; 219:123-131. [DOI: 10.1016/j.micres.2018.11.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 10/16/2018] [Accepted: 11/22/2018] [Indexed: 11/22/2022]
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42
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Yang Q, Yang Y, Xu R, Lv H, Liao H. Genetic Analysis and Mapping of QTLs for Soybean Biological Nitrogen Fixation Traits Under Varied Field Conditions. FRONTIERS IN PLANT SCIENCE 2019; 10:75. [PMID: 30774643 PMCID: PMC6367678 DOI: 10.3389/fpls.2019.00075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/17/2019] [Indexed: 06/01/2023]
Abstract
Soybean is an important economic and green manure crop that is widely used in intercropping and rotation systems due to its high biological nitrogen fixation (BNF) capacity and the resulting reduction in N fertilization. However, the genetic mechanisms underlying soybean BNF are largely unknown. Here, two soybean parent genotypes contrasting in BNF traits and 168 F9:11 recombinant inbred lines (RILs) were evaluated under four conditions in the field. The parent FC1 always produced more big nodules, yet fewer nodules in total than the parent FC2 in the field. Furthermore, nodulation in FC1 was more responsive to environmental changes than that in FC2. Broad-sense heritability (h2 b ) for all BNF traits varied from 0.48 to 0.87, which suggests that variation in the observed BNF traits was primarily determined by genotype. Moreover, two new QTLs for BNF traits, qBNF-16 and qBNF-17, were identified in this study. The qBNF-16 locus was detected under all of the four tested conditions, where it explained 15.9-59.0% of phenotypic variation with LOD values of 6.31-32.5. Meanwhile qBNF-17 explained 12.6-18.6% of observed variation with LOD values of 4.93-7.51. Genotype group analysis indicated that the FC1 genotype of qBNF-16 primarily affected nodule size (NS), while the FC2 genotype of qBNF-16 promoted nodule number (NN). On the other hand, the FC1 genotype of qBNF-17 influenced NN and the FC2 genotype of qBNF-17 impacted NS. The results on the whole suggest that these two QTLs might be valuable markers for breeding elite soybean varieties with high BNF capacities.
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Yu F, Jing X, Li X, Wang H, Chen H, Zhong L, Yin J, Pan D, Yin Y, Fu J, Xia L, Bian X, Tu Q, Zhang Y. Recombineering Pseudomonas protegens CHA0: An innovative approach that improves nitrogen fixation with impressive bactericidal potency. Microbiol Res 2019; 218:58-65. [DOI: 10.1016/j.micres.2018.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 08/06/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
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44
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Screening, plant growth promotion and root colonization pattern of two rhizobacteria (Pseudomonas fluorescens Ps006 and Bacillus amyloliquefaciens Bs006) on banana cv. Williams (Musa acuminata Colla). Microbiol Res 2018; 220:12-20. [PMID: 30744815 DOI: 10.1016/j.micres.2018.11.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/10/2018] [Accepted: 11/22/2018] [Indexed: 11/22/2022]
Abstract
Banana is the second largest export crop in Colombia. To meet the demand of international markets, high amounts of chemical fertilizers are required, which represent high costs and can be hazardous to the environment. Plant growth promoting rhizobacteria (PGPR) can, at least partially, replace chemical fertilizers. In this paper, we evaluated the effect of nine PGPR of the genera Bacillus and Pseudomonas on banana growth. Banana seedlings were produced through tissue culture and acclimatized in the greenhouse core. Plants were inoculated with the rhizobacteria and growth parameters (plant height, leaf number, leaf area, pseudostem thickness, root and shoot fresh weight, root and shoot dry weight) were assessed after 55 days. The two best performing PGPR, Bs006 and Ps006 previously identified as Bacillus amyloliquefaciens and Pseudomonas fluorescens, respectively, promoted banana growth similarly or even slightly superior to 100% chemical fertilization, and were selected for further characterization of root colonization by both eletron microscopy and confocal microscopy of fluorescence in situ hybridization (FISH)-stained root tissues. Both P. fluorescens Ps006 and B. amyloquifaciens Bs006 showed ability to colonize banana roots, but Bs006 appeared faster than Ps006 in the colonization dynamics. This work demonstrated that inoculation of rhizobacteria Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006 could partially replace the chemical fertilization of tissue cultured banana plants, and therefore could be used for the formulation of a new biofertilizer.
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Jing X, Cui Q, Li X, Yin J, Ravichandran V, Pan D, Fu J, Tu Q, Wang H, Bian X, Zhang Y. Engineering Pseudomonas protegens Pf-5 to improve its antifungal activity and nitrogen fixation. Microb Biotechnol 2018; 13:118-133. [PMID: 30461205 PMCID: PMC6984399 DOI: 10.1111/1751-7915.13335] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/21/2018] [Accepted: 10/21/2018] [Indexed: 11/26/2022] Open
Abstract
In agricultural production, sustainability is currently one of the most significant concerns. The genetic modification of plant growth‐promoting rhizobacteria may provide a novel way to use natural bacteria as microbial inoculants. In this study, the root‐colonizing strain Pseudomonas protegens Pf‐5 was genetically modified to act as a biocontrol agent and biofertilizer with biological nitrogen fixation activity. Genetic inactivation of retS enhanced the production of 2,4‐diacetylphloroglucinol, which contributed for the enhanced antifungal activity. Then, the entire nitrogenase island with native promoter from Pseudomonas stutzeri DSM4166 was introduced into a retS mutant strain for expression. Root colonization patterns assessed via confocal laser scanning microscopy confirmed that GFP‐tagged bacterial were mainly located on root surfaces and at the junctions between epidermal root cells. Moreover, under pathogen and N‐limited double treatment conditions, the fresh weights of seedlings inoculated with the recombinant retS mutant‐nif strain were increased compared with those of the control. In conclusion, this study has innovatively developed an eco‐friendly alternative to the agrochemicals that will benefit global plant production significantly.
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Affiliation(s)
- Xiaoshu Jing
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Qingwen Cui
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Jia Yin
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Vinothkannan Ravichandran
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Deng Pan
- Jinan Yian Biology Institute, Shandong Yian Biological Engineering Co. Ltd., Jinan, 250100, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Qiang Tu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Xiaoying Bian
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
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Ke X, Feng S, Wang J, Lu W, Zhang W, Chen M, Lin M. Effect of inoculation with nitrogen-fixing bacterium Pseudomonas stutzeri A1501 on maize plant growth and the microbiome indigenous to the rhizosphere. Syst Appl Microbiol 2018; 42:248-260. [PMID: 30477902 DOI: 10.1016/j.syapm.2018.10.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/21/2018] [Accepted: 10/31/2018] [Indexed: 12/12/2022]
Abstract
Plant growth promoting diazotrophs with the ability to associate with plant roots are in common use as inoculants to benefit crop yield and to mitigate chemical nitrogen fertilization. However, limited information is available in understanding to what extent the plant growth-promoting effect of the inoculum has on the plant's nitrogen acquisition as well as on the impact of inoculation on the indigenous rhizosphere microbial population. Here we reported on experiments that assessed how endophytic Pseudomonas stutzeri A1501 inoculated on maize improved plant growth and plant nitrogen content using a 15N dilution technique under two water regime conditions. The effects of inoculation and different water regimes were also assessed for the maize rhizospheric and surface soil communities by MiSeq community sequencing combined with qPCR of functional genes and transcripts (nifH and amoA) related to nitrogen cycling. Results support maize inoculated with P. stutzeri A1501 grew better and accumulated more nitrogen with a lower δ15N signature after 60 days than did plants inoculated with nifH-mutant and sterilized A1501 cells (non N2-fixing controls). Inoculant contribution to the plant was estimated to range from 0.30 to 0.82g N/plant, depending on water conditions. Inoculation with P. stutzeri A1501 significantly altered the composition of the diazotrophic community that P. stutzeri became dominant in the rhizosphere, and also increased the population of indigenous diazotrophs and ammonia oxidizers and functional genes transcripts. Redundancy analysis revealed that soil compartment and A1501 inoculation treatments were the main factors affecting the distribution of the diazotrophic community.
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Affiliation(s)
- Xiubin Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Feng
- Life Science and Engineering College, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Life Science and Engineering College, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Stritzler M, Soto G, Ayub N. Plant Growth-Promoting Genes can Switch to be Virulence Factors via Horizontal Gene Transfer. MICROBIAL ECOLOGY 2018; 76:579-583. [PMID: 29476343 DOI: 10.1007/s00248-018-1163-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
There are increasing evidences that horizontal gene transfer (HGT) is a critical mechanism of bacterial evolution, while its complete impact remains unclear. A main constraint of HGT effects on microbial evolution seems to be the conservation of the function of the horizontally transferred genes. From this perspective, inflexible nomenclature and functionality criteria have been established for some mobile genetic elements such as pathogenic and symbiotic islands. Adhesion is a universal prerequisite for both beneficial and pathogenic plant-microbe interactions, and thus, adhesion systems (e.g., the Lap cluster) are candidates to have a dual function depending on the genomic background. In this study, we showed that the virulent factor Lap of the phytopathogen Erwinia carotovora SCRI1043, which is located within a genomic island, was acquired by HGT and probably derived from Pseudomonas. The transformation of the phytopathogen Erwinia pyrifoliae Ep1/96 with the beneficial factor Lap from the plant growth-promoting bacterium Pseudomonas fluorescens Pf-5 significantly increased its natural virulence, experimentally recapitulating the beneficial-to-virulence functional switch of the Lap cluster via HGT. To our knowledge, this is the first report of a functional switch of an individual gene or a cluster of genes mediated by HGT.
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Affiliation(s)
- Margarita Stritzler
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), De los Reseros S/N, C25(1712), Castelar, Buenos Aires, Argentina
| | - Gabriela Soto
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), De los Reseros S/N, C25(1712), Castelar, Buenos Aires, Argentina
| | - Nicolás Ayub
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina.
- Instituto Nacional de Tecnología Agropecuaria (INTA), De los Reseros S/N, C25(1712), Castelar, Buenos Aires, Argentina.
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Rosenblueth M, Ormeño-Orrillo E, López-López A, Rogel MA, Reyes-Hernández BJ, Martínez-Romero JC, Reddy PM, Martínez-Romero E. Nitrogen Fixation in Cereals. Front Microbiol 2018; 9:1794. [PMID: 30140262 PMCID: PMC6095057 DOI: 10.3389/fmicb.2018.01794] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/17/2018] [Indexed: 01/30/2023] Open
Abstract
Cereals such as maize, rice, wheat and sorghum are the most important crops for human nutrition. Like other plants, cereals associate with diverse bacteria (including nitrogen-fixing bacteria called diazotrophs) and fungi. As large amounts of chemical fertilizers are used in cereals, it has always been desirable to promote biological nitrogen fixation in such crops. The quest for nitrogen fixation in cereals started long ago with the isolation of nitrogen-fixing bacteria from different plants. The sources of diazotrophs in cereals may be seeds, soils, and even irrigation water and diazotrophs have been found on roots or as endophytes. Recently, culture-independent molecular approaches have revealed that some rhizobia are found in cereal plants and that bacterial nitrogenase genes are expressed in plants. Since the levels of nitrogen-fixation attained with nitrogen-fixing bacteria in cereals are not high enough to support the plant’s needs and never as good as those obtained with chemical fertilizers or with rhizobium in symbiosis with legumes, it has been the aim of different studies to increase nitrogen-fixation in cereals. In many cases, these efforts have not been successful. However, new diazotroph mutants with enhanced capabilities to excrete ammonium are being successfully used to promote plant growth as commensal bacteria. In addition, there are ambitious projects supported by different funding agencies that are trying to genetically modify maize and other cereals to enhance diazotroph colonization or to fix nitrogen or to form nodules with nitrogen-fixing symbiotic rhizobia.
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Affiliation(s)
- Mónica Rosenblueth
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ernesto Ormeño-Orrillo
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Aline López-López
- Centro de Investigación en Genética y Ambiente, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Marco A Rogel
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | | | - Pallavolu M Reddy
- The Energy and Resources Institute, India Habitat Centre, New Delhi, India
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Stritzler M, Elba P, Berini C, Gomez C, Ayub N, Soto G. High-quality forage production under salinity by using a salt-tolerant AtNXH1-expressing transgenic alfalfa combined with a natural stress-resistant nitrogen-fixing bacterium. J Biotechnol 2018; 276-277:42-45. [DOI: 10.1016/j.jbiotec.2018.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 03/26/2018] [Accepted: 04/18/2018] [Indexed: 11/16/2022]
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Plant growth-promoting bacterium Pseudomonas fluorescens FR1 secrets a novel type of extracellular polyhydroxybutyrate polymerase involved in abiotic stress response in plants. Biotechnol Lett 2018; 40:1419-1423. [DOI: 10.1007/s10529-018-2576-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 05/22/2018] [Indexed: 10/16/2022]
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