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Bernardes MB, Dal’Rio I, Rodrigues Coelho MR, Seldin L. Response of sweet potato cultivars to Bacillus velezensis T149-19 and Bacillus safensis T052-76 used as biofertilizers. Heliyon 2024; 10:e34377. [PMID: 39104509 PMCID: PMC11298936 DOI: 10.1016/j.heliyon.2024.e34377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 08/07/2024] Open
Abstract
The global market of sweet potato (Ipomoea batatas (L.) Lam.) is continuously growing and, consequently, demands greater productivity from the agricultural sector. The use of biofertilizers facilitates plant growth by making essential nutrients available to crops or providing resistance against different abiotic and biotic factors. The strains Bacillus safensis T052-76 and Bacillus velezensis T149-19 have previously been inoculated in the sweet potato cultivar Ourinho, showing positive effects on plant shoot growth and inhibiting the phytopathogen Plenodomus destruens. To elucidate the effects of these strains on sweet potato growth, four different cultivars of sweet potato were selected: Capivara, IAPAR 69, Rosinha de Verdan and Roxa. The plants were grown in pots in a greenhouse and inoculated with the combined strains according to a randomized block design. A control (without the inoculation of both strains) was also used. A slight positive effect of the inoculation of the two Bacillus strains was observed on the aerial parts of some of the cultivars. An increase in the fresh weight of the sweet potatoes of the inoculated plants was obtained, varying from 2.7 to 11.4 %. The number of sweet potatoes obtained from the inoculated cultivars IAPAR 69 and Roxa increased 15.2 % and 16.7 %, respectively. The rhizosphere soil of each cultivar was further sampled for DNA extraction, and the 16S rRNA gene metabarcoding technique was used to determine how the introduction of these Bacillus strains influenced the rhizosphere bacterial community. The bacterial communities of the four different cultivars were dominated by Actinobacteria, Proteobacteria and Firmicutes. Nonmetric multidimensional scaling (NMDS) revealed that the rhizosphere bacterial communities of plants inoculated with Bacillus strains were more similar to each other than to the bacterial communities of uninoculated plants. This study highlights the contribution of these Bacillus strains to the promotion of sweet potato growth.
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Affiliation(s)
- Matheus Barbosa Bernardes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Isabella Dal’Rio
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Lamichhane JR, Barbetti MJ, Chilvers MI, Pandey AK, Steinberg C. Exploiting root exudates to manage soil-borne disease complexes in a changing climate. Trends Microbiol 2024; 32:27-37. [PMID: 37598008 DOI: 10.1016/j.tim.2023.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/21/2023]
Abstract
Ongoing climate change will both profoundly impact land-use (e.g., changes in crop species or cultivar and cropping practices) and abiotic factors (e.g., moisture and temperature), which will in turn alter plant-microorganism interactions in soils, including soil-borne pathogens (i.e., plant pathogenic bacteria, fungi, oomycetes, viruses, and nematodes). These pathogens often cause soil-borne disease complexes, which, due to their complexity, frequently remain undiagnosed and unmanaged, leading to chronic yield and quality losses. Root exudates are a complex group of organic substances released in the rhizosphere with potential to recruit, repel, stimulate, inhibit, or kill other organisms, including the detrimental ones. An improved understanding of how root exudates affect interspecies and/or interkingdom interactions in the rhizosphere under ongoing climate change is a prerequisite to effectively manage plant-associated microbes, including those causing diseases.
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Affiliation(s)
- Jay Ram Lamichhane
- INRAE, Université Fédérale de Toulouse, UMR AGIR, F-31326 Castanet-Tolosan Cedex, France.
| | - Martin J Barbetti
- School of Agriculture and Environment and the UWA Institute of Agriculture, University of Western Australia, Western Australia 6009, Australia
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Abhay K Pandey
- Department of Mycology & Microbiology, Tea Research Association, North Bengal Regional R & D Center, Nagrakata 735225, West Bengal, India
| | - Christian Steinberg
- Agroécologie, INRAE Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
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Boubsi F, Hoff G, Arguelles Arias A, Steels S, Andrić S, Anckaert A, Roulard R, Rigolet A, van Wuytswinkel O, Ongena M. Pectic homogalacturonan sensed by Bacillus acts as host associated cue to promote establishment and persistence in the rhizosphere. iScience 2023; 26:107925. [PMID: 37790276 PMCID: PMC10543691 DOI: 10.1016/j.isci.2023.107925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/19/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
Bacillus velezensis isolates are among the most promising plant-associated beneficial bacteria used as biocontrol agents. However, various aspects of the chemical communication between the plant and these beneficials, determining root colonization ability, remain poorly described. Here we investigated the molecular basis of such interkingdom interaction occurring upon contact between Bacillus velezensis and its host via the sensing of pectin backbone homogalacturonan (HG). We showed that B. velezensis stimulates key developmental traits via a dynamic process involving two conserved pectinolytic enzymes. This response integrates transcriptional changes leading to the switch from planktonic to sessile cells, a strong increase in biofilm formation, and an accelerated sporulation dynamics while conserving the potential to efficiently produce specialized secondary metabolites. As a whole, we anticipate that this response of Bacillus to cell wall-derived host cues contributes to its establishment and persistence in the competitive rhizosphere niche and ipso facto to its activity as biocontrol agent.
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Affiliation(s)
- Farah Boubsi
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Grégory Hoff
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Anthony Arguelles Arias
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Sébastien Steels
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Sofija Andrić
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Adrien Anckaert
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Romain Roulard
- UMRT INRAe 1158 Plant Biology and Innovation, University of Picardie Jules Verne, UFR des Sciences, 80039 Amiens, France
| | - Augustin Rigolet
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Olivier van Wuytswinkel
- UMRT INRAe 1158 Plant Biology and Innovation, University of Picardie Jules Verne, UFR des Sciences, 80039 Amiens, France
| | - Marc Ongena
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
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López-Bucio J, Ortiz-Castro R, Magaña-Dueñas V, García-Cárdenas E, Jiménez-Vázquez KR, Raya-González J, Pelagio-Flores R, Ibarra-Laclette E, Herrera-Estrella L. Pseudomonas aeruginosa LasI-dependent plant growth promotion requires the host nitrate transceptor AtNRT1.1/CHL1 and the nitrate reductases NIA1 and NIA2. PLANTA 2023; 258:80. [PMID: 37715847 DOI: 10.1007/s00425-023-04236-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 09/04/2023] [Indexed: 09/18/2023]
Abstract
MAIN CONCLUSION In P. aeruginosa, mutation of the gene encoding N-acyl-L-homoserine lactone synthase LasI drives defense and plant growth promotion, and this latter trait requires adequate nitrate nutrition. Cross-kingdom communication with bacteria is crucial for plant growth and productivity. Here, we show a strong induction of genes for nitrate uptake and assimilation in Arabidopsis seedlings co-cultivated with P. aeruginosa WT (PAO1) or ΔlasI mutants defective on the synthesis of the quorum-sensing signaling molecule N-(3-oxododecanoyl)-L-homoserine lactone. Along with differential induction of defense-related genes, the change from plant growth repression to growth promotion upon bacterial QS disruption, correlated with upregulation of the dual-affinity nitrate transceptor CHL1/AtNRT1/NPF6.3 and the nitrate reductases NIA1 and NIA2. CHL1-GUS was induced in Arabidopsis primary root tips after transfer onto P. aeruginosa ΔlasI streaks at low and high N availability, whereas this bacterium required high concentrations of nitrogen to potentiate root and shoot biomass production and to improve root branching. Arabidopsis chl1-5 and chl1-12 mutants and double mutants in NIA1 and NIA2 nitrate reductases showed compromised growth under low nitrogen availability and failed to mount an effective growth promotion and root branching response even at high NH4NO3. WT P. aeruginosa PAO1 and P. aeruginosa ΔlasI mutant promoted the accumulation of nitric oxide (NO) in roots of both the WT and nia1nia2 double mutants, whereas NO donors SNP or SNAP did not improve growth or root branching in nia1nia2 double mutants with or without bacterial cocultivation. Thus, inoculation of Arabidopsis roots with P. aeruginosa drives gene expression for improved nitrogen acquisition and this macronutrient is critical for the plant growth-promoting effects upon disruption of the LasI quorum-sensing system.
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Affiliation(s)
- José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico.
| | - Randy Ortiz-Castro
- Red de estudios moleculares avanzados, Instituto de Ecología A. C., Carretera Antigua a Coatepec 351, El Haya, 91070, Xalapa, Veracruz, Mexico
| | - Viridiana Magaña-Dueñas
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico
| | - Elizabeth García-Cárdenas
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico
| | - Kirán Rubí Jiménez-Vázquez
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico
| | - Javier Raya-González
- Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Tzintzunzan 173, Col. Matamoros, 58240, Morelia, Michoacán, Mexico
| | - Ramón Pelagio-Flores
- Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Tzintzunzan 173, Col. Matamoros, 58240, Morelia, Michoacán, Mexico
| | - Enrique Ibarra-Laclette
- Red de estudios moleculares avanzados, Instituto de Ecología A. C., Carretera Antigua a Coatepec 351, El Haya, 91070, Xalapa, Veracruz, Mexico
| | - Luis Herrera-Estrella
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Campus Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico
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5
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Sánchez-Gil JJ, Poppeliers SWM, Vacheron J, Zhang H, Odijk B, Keel C, de Jonge R. The conserved iol gene cluster in Pseudomonas is involved in rhizosphere competence. Curr Biol 2023; 33:3097-3110.e6. [PMID: 37419116 DOI: 10.1016/j.cub.2023.05.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/25/2023] [Accepted: 05/24/2023] [Indexed: 07/09/2023]
Abstract
The Pseudomonas genus has shown great potential as a sustainable solution to support agriculture through its plant-growth-promoting and biocontrol activities. However, their efficacy as bioinoculants is limited by unpredictable colonization in natural conditions. Our study identifies the iol locus, a gene cluster in Pseudomonas involved in inositol catabolism, as a feature enriched among superior root colonizers in natural soil. Further characterization revealed that the iol locus increases competitiveness, potentially caused by an observed induction of swimming motility and the production of fluorescent siderophore in response to inositol, a plant-derived compound. Public data analyses indicate that the iol locus is broadly conserved in the Pseudomonas genus and linked to diverse host-microbe interactions. Together, our findings suggest the iol locus as a potential target for developing more effective bioinoculants for sustainable agriculture.
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Affiliation(s)
- Juan J Sánchez-Gil
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Sanne W M Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Hao Zhang
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Bart Odijk
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands.
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Gómez-Godínez LJ, Aguirre-Noyola JL, Martínez-Romero E, Arteaga-Garibay RI, Ireta-Moreno J, Ruvalcaba-Gómez JM. A Look at Plant-Growth-Promoting Bacteria. PLANTS (BASEL, SWITZERLAND) 2023; 12:1668. [PMID: 37111891 PMCID: PMC10145503 DOI: 10.3390/plants12081668] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/06/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Bacteria have been used to increase crop yields. For their application on crops, bacteria are provided in inoculant formulations that are continuously changing, with liquid- and solid-based products. Bacteria for inoculants are mainly selected from natural isolates. In nature, microorganisms that favor plants exhibit various strategies to succeed and prevail in the rhizosphere, such as biological nitrogen fixation, phosphorus solubilization, and siderophore production. On the other hand, plants have strategies to maintain beneficial microorganisms, such as the exudation of chemoattractanst for specific microorganisms and signaling pathways that regulate plant-bacteria interactions. Transcriptomic approaches are helpful in attempting to elucidate plant-microorganism interactions. Here, we present a review of these issues.
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Affiliation(s)
- Lorena Jacqueline Gómez-Godínez
- Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tepatitlán de Morelos 47600, Jalisco, Mexico
| | - José Luis Aguirre-Noyola
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Ramón Ignacio Arteaga-Garibay
- Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tepatitlán de Morelos 47600, Jalisco, Mexico
| | - Javier Ireta-Moreno
- Centro de Investigación Regional Pacífico Centro, Centro Altos Jalisco, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tepatitlán de Morelos 2470, Jalisco, Mexico
| | - José Martín Ruvalcaba-Gómez
- Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tepatitlán de Morelos 47600, Jalisco, Mexico
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7
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Han L, Zhang H, Bai X, Jiang B. The peanut root exudate increases the transport and metabolism of nutrients and enhances the plant growth-promoting effects of burkholderia pyrrocinia strain P10. BMC Microbiol 2023; 23:85. [PMID: 36991332 PMCID: PMC10061817 DOI: 10.1186/s12866-023-02818-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/10/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Burkholderia pyrrocinia strain P10 is a plant growth-promoting rhizobacterium (PGPR) that can substantially increase peanut growth. However, the mechanisms and pathways involved in the interaction between B. pyrrocinia P10 and peanut remain unclear. To clarify complex plant-PGPR interactions and the growth-promoting effects of PGPR strains, the B. pyrrocinia P10 transcriptome changes in response to the peanut root exudate (RE) were elucidated and the effects of RE components on biofilm formation and indole-3-acetic acid (IAA) secretion were analyzed. RESULTS During the early interaction phase, the peanut RE enhanced the transport and metabolism of nutrients, including carbohydrates, amino acids, nitrogen, and sulfur. Although the expression of flagellar assembly-related genes was down-regulated, the expression levels of other genes involved in biofilm formation, quorum sensing, and Type II, III, and VI secretion systems were up-regulated, thereby enabling strain P10 to outcompete other microbes to colonize the peanut rhizosphere. The peanut RE also improved the plant growth-promoting effects of strain P10 by activating the expression of genes associated with siderophore biosynthesis, IAA production, and phosphorus solubilization. Additionally, organic acids and amino acids were identified as the dominant components in the peanut RE. Furthermore, strain P10 biofilm formation was induced by malic acid, oxalic acid, and citric acid, whereas IAA secretion was promoted by the alanine, glycine, and proline in the peanut RE. CONCLUSION The peanut RE positively affects B. pyrrocinia P10 growth, while also enhancing colonization and growth-promoting effects during the early interaction period. These findings may help to elucidate the mechanisms underlying complex plant-PGPR interactions, with potential implications for improving the applicability of PGPR strains.
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Affiliation(s)
- Lizhen Han
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China.
| | - Hong Zhang
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China
| | - Xue Bai
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China
| | - Biao Jiang
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China
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Korangi Alleluya V, Argüelles Arias A, Ribeiro B, De Coninck B, Helmus C, Delaplace P, Ongena M. Bacillus lipopeptide-mediated biocontrol of peanut stem rot caused by Athelia rolfsii. FRONTIERS IN PLANT SCIENCE 2023; 14:1069971. [PMID: 36890892 PMCID: PMC9986434 DOI: 10.3389/fpls.2023.1069971] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Peanut (Arachis hypogaea L.) is a widespread oilseed crop of high agricultural importance in tropical and subtropical areas. It plays a major role in the food supply in the Democratic Republic of Congo (DRC). However, one major constraint in the production of this plant is the stem rot (white mold or southern blight) disease caused by Athelia rolfsii which is so far controlled mainly using chemicals. Considering the harmful effect of chemical pesticides, the implementation of eco-friendly alternatives such as biological control is required for disease management in a more sustainable agriculture in the DRC as in the other developing countries concerned. Bacillus velezensis is among the rhizobacteria best described for its plant protective effect notably due to the production of a wide range of bioactive secondary metabolites. In this work, we wanted to evaluate the potential of B. velezensis strain GA1 at reducing A. rolfsii infection and to unravel the molecular basis of the protective effect. RESULTS AND DISCUSSION Upon growth under the nutritional conditions dictated by peanut root exudation, the bacterium efficiently produces the three types of lipopeptides surfactin, iturin and fengycin known for their antagonistic activities against a wide range of fungal phytopathogens. By testing a range of GA1 mutants specifically repressed in the production of those metabolites, we point out an important role for iturin and another unidentified compound in the antagonistic activity against the pathogen. Biocontrol experiments performed in greenhouse further revealed the efficacy of B. velezensis to reduce peanut disease caused by A. rolfsii both via direct antagonism against the fungus and by stimulating systemic resistance in the host plant. As treatment with pure surfactin yielded a similar level of protection, we postulate that this lipopeptide acts as main elicitor of peanut resistance against A. rolfsii infection.
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Affiliation(s)
- Virginie Korangi Alleluya
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Chemical and Agricultural Industries, Faculty of Agricultural Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Anthony Argüelles Arias
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Bianca Ribeiro
- Division of Plant Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Barbara De Coninck
- Division of Plant Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Catherine Helmus
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Pierre Delaplace
- Plant biology Unit, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
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9
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Lohse M, Santangeli M, Steininger-Mairinger T, Oburger E, Reemtsma T, Lechtenfeld OJ, Hann S. The effect of root hairs on exudate composition: a comparative non-targeted metabolomics approach. Anal Bioanal Chem 2023; 415:823-840. [PMID: 36547703 PMCID: PMC9883335 DOI: 10.1007/s00216-022-04475-9] [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: 08/12/2022] [Revised: 11/10/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
Root exudation is a major pathway of organic carbon input into soils. It affects soil physical properties, element solubility as well as speciation, and impacts the microbial community in the rhizosphere. Root exudates contain a large number of primary and secondary plant metabolites, and the amount and composition are highly variable depending on plant species and developmental stage. Detailed information about exudate composition will allow for a better understanding of exudate-driven rhizosphere processes and their feedback loops. Although non-targeted metabolomics by high-resolution mass spectrometry is an established tool to characterize root exudate composition, the extent and depth of the information obtained depends strongly on the analytical approach applied. Here, two genotypes of Zea mays L., differing in root hair development, were used to compare six mass spectrometric approaches for the analysis of root exudates. Reversed-phase liquid chromatography and hydrophilic interaction liquid chromatography combined with time-of-flight mass spectrometry (LC-TOF-MS), as well as direct infusion Fourier-transform ion cyclotron resonance mass spectrometry (DI-FT-ICR-MS), were applied with positive and negative ionization mode. By using the same statistical workflow, the six approaches resulted in different numbers of detected molecular features, ranging from 176 to 889, with a fraction of 48 to 69% of significant features (fold change between the two genotypes of > 2 and p-value < 0.05). All approaches revealed the same trend between genotypes, namely up-regulation of most metabolites in the root hair defective mutant (rth3). These results were in agreement with the higher total carbon and nitrogen exudation rate of the rth3-mutant as compared to the corresponding wild-type maize (WT). However, only a small fraction of features were commonly found across the different analytical approaches (20-79 features, 13-31% of the rth3-mutant up-regulated molecular formulas), highlighting the need for different mass spectrometric approaches to obtain a more comprehensive view into the composition of root exudates. In summary, 111 rth3-mutant up-regulated compounds (92 different molecular formulas) were detected with at least two different analytical approaches, while no WT up-regulated compound was found by both, LC-TOF-MS and DI-FT-ICR-MS. Zea mays L. exudate features obtained with multiple analytical approaches in our study were matched against the metabolome database of Zea mays L. (KEGG) and revealed 49 putative metabolites based on their molecular formula.
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Affiliation(s)
- Martin Lohse
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Michael Santangeli
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna (BOKU), 3430, Tulln an Der Donau, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Teresa Steininger-Mairinger
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Eva Oburger
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna (BOKU), 3430, Tulln an Der Donau, Austria.
| | - Thorsten Reemtsma
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
- Institute of Analytical Chemistry, University of Leipzig, 04103, Leipzig, Germany
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany.
- ProVIS, Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research, UFZ, 04318, Leipzig, Germany.
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
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Jiang B, Long C, Xu Y, Han L. Molecular mechanism of Tsukamurella tyrosinosolvens strain P9 in response to root exudates of peanut. Arch Microbiol 2023; 205:48. [PMID: 36595098 DOI: 10.1007/s00203-022-03387-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/19/2022] [Accepted: 12/22/2022] [Indexed: 01/04/2023]
Abstract
Tsukamurella tyrosinosolvens strain P9 is a rare actinomycete with plant growth-promoting properties and can improve the growth of peanut. We analyzed the differentially expressed genes (DEGs) of P9 under the influence of peanut root exudates from RNA-sequencing data and analyzed the effects of root exudates and their organic acid and amino acid components on the growth and growth-promoting effects of this strain to explore the molecular mechanism of the P9 response. The results showed that peanut root exudates promoted the growth and growth-promoting activity of P9. Transcriptome analysis revealed 126 DEGs in P9, comprising 81 up-regulated and 45 down-regulated genes. The DEGs were significantly enriched in 17 KEGG metabolic pathways, including arginine biosynthesis, butyric acid metabolism, fatty acid degradation, and tryptophan metabolism. Peanut root exudates induced up-regulation of nutrient transport, carbohydrate metabolism and energy production, siderophore and IAA biosynthesis, adhesion, and biofilm formation, and down-regulation of arginine biosynthesis and the urea cycle in P9. Organic acids and amino acids are the major components of peanut root exudates. Glycine, proline, and alanine promoted the growth and IAA secretion of P9. Proline, alanine (40 mM), and oxalic acid significantly enhanced siderophore biosynthesis, whereas citric acid, oxalic acid, and malic acid significantly promoted biofilm formation of P9. This study clarifies the response of T. tyrosinosolvens P9 to peanut root exudates at the molecular level, examining the molecular basis of the relationship between P9 and peanut, and provides a theoretical foundation for improved exertion of the growth-promoting properties of P9.
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Affiliation(s)
- Biao Jiang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Changmei Long
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yu Xu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Lizhen Han
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China.
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11
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The key role of indole-3-acetic acid biosynthesis by Bacillus thuringiensis RZ2MS9 in promoting maize growth revealed by the ipdC gene knockout mediated by the CRISPR-Cas9 system. Microbiol Res 2022; 266:127218. [DOI: 10.1016/j.micres.2022.127218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 09/16/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022]
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12
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Sivakumar R, Gunasekaran P, Rajendhran J. Extracytoplasmic sigma factor AlgU contributes to fitness of Pseudomonas aeruginosa PGPR2 during corn root colonization. Mol Genet Genomics 2022; 297:1537-1552. [PMID: 35980488 DOI: 10.1007/s00438-022-01938-7] [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: 08/25/2020] [Accepted: 07/29/2022] [Indexed: 11/28/2022]
Abstract
In bacteria, sigma factors are crucial in determining the plasticity of core RNA polymerase (RNAP) while promoter recognition during transcription initiation. This process is modulated through an intricate regulatory network in response to environmental cues. Previously, an extracytoplasmic function (ECF) sigma factor, AlgU, was identified to positively influence the fitness of Pseudomonas aeruginosa PGPR2 during corn root colonization. In this study, we report that the inactivation of the algU gene encoded by PGPR2_23995 hampers the root colonization ability of PGPR2. An insertion mutant in the algU gene was constructed by allele exchange mutagenesis. The mutant strains displayed threefold decreased root colonization efficiency compared with the wild-type strain when inoculated individually and in the competition assay. The mutant strain was more sensitive to osmotic and antibiotic stresses and showed higher resistance to oxidative stress. On the other hand, the mutant strain showed increased biofilm formation on the abiotic surface, and the expression of the pelB and pslA genes involved in the biofilm matrix formation were up-regulated. In contrast, the expression of algD, responsible for alginate production, was significantly down-regulated in the mutant strain, which is directly regulated by the AlgU sigma factor. The mutant strain also displayed altered motility. The expression of RNA binding protein RsmA was also impeded in the mutant strain. Further, the transcript levels of genes associated with the type III secretion system (T3SS) were analyzed, which revealed a significant down-regulation in the mutant strain. These results collectively provide evidence for the regulatory role of the AlgU sigma factor in modulating gene expression during root colonization.
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Affiliation(s)
- Ramamoorthy Sivakumar
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India
| | | | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India.
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13
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Orozco-Mosqueda MDC, Fadiji AE, Babalola OO, Glick BR, Santoyo G. Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health. Microbiol Res 2022; 263:127137. [PMID: 35905581 DOI: 10.1016/j.micres.2022.127137] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/17/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.
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Affiliation(s)
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico.
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14
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Formation and Microbial Composition of Biofilms in Drip Irrigation System under Three Reclaimed Water Conditions. WATER 2022. [DOI: 10.3390/w14081216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
As the second source of water for cities, reclaimed water (RW) has become an effective solution to the problem of water scarcity in modern agriculture. However, the formation of biofilm in an RW distribution system seriously affects the performance of the system and has become a technical challenge in RW utilization. In this study, we first showed that several water quality parameters, including five-day biochemical oxygen demand (BOD5), total bacteria count (TB), total nitrogen (TN), and Cl− were the main factors affecting biofilm accumulation in the drip irrigation system (DIS), with the correlation coefficient averaging above 0.85. Second, after 392 to 490 h of system operation, the total biomass and extracellular polymer (EPS) accumulation rate of biofilms increased to a maximum of 0.72 g/m2·h and 0.027g/m2·h, respectively, making this time point a critical point for controlling biofilm accumulation and clogging of the system. Third, we examined changes in biofilm microbial composition over time on Illumina’s MiSeq platform. High throughput sequencing data showed that bacterial community structure and microbial network interaction and modularity changed significantly between 392 and 490 h, resulting in maximum microbial diversity and community richness at 490 h. Spearman correlation analyses between genera revealed that Sphingomonas and Rhodococcus promote biofilm formation due to their hydrophobicity, while Bacillus, Mariniradius, and Arthronema may inhibit biofilm formation due to their antagonistic effects on other genera. In conclusion, this work has clarified the accumulation process and compositional changes of biofilms in agriculture DIS under different RW conditions, which provides a basis for improving RW utilization efficiency and reducing system maintenance costs.
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15
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Lopez-Guerrero MG, Wang P, Phares F, Schachtman DP, Alvarez S, van Dijk K. A glass bead semi-hydroponic system for intact maize root exudate analysis and phenotyping. PLANT METHODS 2022; 18:25. [PMID: 35246193 PMCID: PMC8897885 DOI: 10.1186/s13007-022-00856-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Although there have been numerous studies describing plant growth systems for root exudate collection, a common limitation is that these systems require disruption of the plant root system to facilitate exudate collection. Here, we present a newly designed semi-hydroponic system that uses glass beads as solid support to simulate soil impedance, which combined with drip irrigation, facilitates growth of healthy maize plants, collection and analysis of root exudates, and phenotyping of the roots with minimal growth disturbance or root damage. RESULTS This system was used to collect root exudates from seven maize genotypes using water or 1 mM CaCl2, and to measure root phenotype data using standard methods and the Digital imaging of root traits (DIRT) software. LC-MS/MS (Liquid Chromatography-Tandem Mass Spectrometry) and GC-MS (Gas Chromatography-Mass Spectrometry) targeted metabolomics platforms were used to detect and quantify metabolites in the root exudates. Phytohormones, some of which are reported in maize root exudates for the first time, the benzoxazinoid DIMBOA (2,4-Dihydroxy-7-methoxy-1,4-benzoxazin-3-one), amino acids, and sugars were detected and quantified. After validating the methodology using known concentrations of standards for the targeted compounds, we found that the choice of the exudate collection solution affected the exudation and analysis of a subset of analyzed metabolites. No differences between collection in water or CaCl2 were found for phytohormones and sugars. In contrast, the amino acids were more concentrated when water was used as the exudate collection solution. The collection in CaCl2 required a clean-up step before MS analysis which was found to interfere with the detection of a subset of the amino acids. Finally, using the phenotypic measurements and the metabolite data, significant differences between genotypes were found and correlations between metabolites and phenotypic traits were identified. CONCLUSIONS A new plant growth system combining glass beads supported hydroponics with semi-automated drip irrigation of sterile solutions was implemented to grow maize plants and collect root exudates without disturbing or damaging the roots. The validated targeted exudate metabolomics platform combined with root phenotyping provides a powerful tool to link plant root and exudate phenotypes to genotype and study the natural variation of plant populations.
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Affiliation(s)
| | - Peng Wang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Felicia Phares
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Sophie Alvarez
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
| | - Karin van Dijk
- Biochemistry Department, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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16
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Madriz-Ordeñana K, Pazarlar S, Jørgensen HJL, Nielsen TK, Zhang Y, Nielsen KL, Hansen LH, Thordal-Christensen H. The Bacillus cereus Strain EC9 Primes the Plant Immune System for Superior Biocontrol of Fusarium oxysporum. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050687. [PMID: 35270157 PMCID: PMC8912794 DOI: 10.3390/plants11050687] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 05/08/2023]
Abstract
Antibiosis is a key feature widely exploited to develop biofungicides based on the ability of biological control agents (BCAs) to produce fungitoxic compounds. A less recognised attribute of plant-associated beneficial microorganisms is their ability to stimulate the plant immune system, which may provide long-term, systemic self-protection against different types of pathogens. By using conventional antifungal in vitro screening coupled with in planta assays, we found antifungal and non-antifungal Bacillus strains that protected the ornamental plant Kalanchoe against the soil-borne pathogen Fusarium oxysporum in experimental and commercial production settings. Further examination of one antifungal and one non-antifungal strain indicated that high protection efficacy in planta did not correlate with antifungal activity in vitro. Whole-genome sequencing showed that the non-antifungal strain EC9 lacked the biosynthetic gene clusters associated with typical antimicrobial compounds. Instead, this bacterium triggers the expression of marker genes for the jasmonic and salicylic acid defence pathways, but only after pathogen challenge, indicating that this strain may protect Kalanchoe plants by priming immunity. We suggest that the stimulation of the plant immune system is a promising mode of action of BCAs for the development of novel biological crop protection products.
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Affiliation(s)
- Kenneth Madriz-Ordeñana
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Plant and Soil Science, University of Copenhagen, 1871 Frederiksberg, Denmark; (S.P.); (H.J.L.J.); (Y.Z.); (H.T.-C.)
- Correspondence:
| | - Sercan Pazarlar
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Plant and Soil Science, University of Copenhagen, 1871 Frederiksberg, Denmark; (S.P.); (H.J.L.J.); (Y.Z.); (H.T.-C.)
| | - Hans Jørgen Lyngs Jørgensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Plant and Soil Science, University of Copenhagen, 1871 Frederiksberg, Denmark; (S.P.); (H.J.L.J.); (Y.Z.); (H.T.-C.)
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Microbial Ecology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark; (T.K.N.); (L.H.H.)
| | - Yingqi Zhang
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Plant and Soil Science, University of Copenhagen, 1871 Frederiksberg, Denmark; (S.P.); (H.J.L.J.); (Y.Z.); (H.T.-C.)
| | | | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Microbial Ecology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark; (T.K.N.); (L.H.H.)
| | - Hans Thordal-Christensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Plant and Soil Science, University of Copenhagen, 1871 Frederiksberg, Denmark; (S.P.); (H.J.L.J.); (Y.Z.); (H.T.-C.)
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17
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A soil-borne Mn(II)-oxidizing bacterium of Providencia sp. exploits a strategy of superoxide production coupled to hydrogen peroxide consumption to generate Mn oxides. Arch Microbiol 2022; 204:168. [DOI: 10.1007/s00203-022-02771-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/08/2021] [Accepted: 01/17/2022] [Indexed: 12/13/2022]
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18
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Herms CH, Hennessy RC, Bak F, Dresbøll DB, Nicolaisen MH. Back to our roots: exploring the role of root morphology as a mediator of beneficial plant-microbe interactions. Environ Microbiol 2022; 24:3264-3272. [PMID: 35106901 PMCID: PMC9543362 DOI: 10.1111/1462-2920.15926] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
Plant breeding for belowground traits that have a positive impact on the rhizosphere microbiome is a promising strategy to sustainably improve crop yields. Root architecture and morphology are understudied plant breeding targets despite their potential to significantly shape microbial community structure and function in the rhizosphere. In this review, we explore the relationship between various root architectural and morphological traits and rhizosphere interactions, focusing on the potential of root diameter to impact the rhizosphere microbiome structure and function while discussing the potential biological and ecological mechanisms underpinning this process. In addition, we propose three future research avenues to drive this research area in an effort to unravel the effect of belowground traits on rhizosphere microbiology. This knowledge will pave the way for new plant breeding strategies that can be exploited for sustainable and high‐yielding crop cultivars.
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Affiliation(s)
- Courtney Horn Herms
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Rosanna Catherine Hennessy
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Frederik Bak
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Dorte Bodin Dresbøll
- Section for Crop Sciences, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 30, Taastrup, 2630, Denmark
| | - Mette Haubjerg Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
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19
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Okoroafor PU, Mann L, Amin Ngu K, Zaffar N, Monei NL, Boldt C, Reitz T, Heilmeier H, Wiche O. Impact of Soil Inoculation with Bacillus amyloliquefaciens FZB42 on the Phytoaccumulation of Germanium, Rare Earth Elements, and Potentially Toxic Elements. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030341. [PMID: 35161323 PMCID: PMC8838376 DOI: 10.3390/plants11030341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 05/21/2023]
Abstract
Bioaugmentation promises benefits for agricultural production as well as for remediation and phytomining approaches. Thus, this study investigated the effect of soil inoculation with the commercially available product RhizoVital®42, which contains Bacillus amyloliquefaciens FZB42, on nutrient uptake and plant biomass production as well as on the phytoaccumulation of potentially toxic elements, germanium, and rare earth elements (REEs). Zea mays and Fagopyrum esculentum were selected as model plants, and after harvest, the element uptake was compared between plants grown on inoculated versus reference soil. The results indicate an enrichment of B. amyloliquefaciens in inoculated soils as well as no significant impact on the inherent bacterial community composition. For F. esculentum, inoculation increased the accumulation of most nutrients and As, Cu, Pb, Co, and REEs (significant for Ca, Cu, and Co with 40%, 2042%, and 383%, respectively), while it slightly decreased the uptake of Ge, Cr, and Fe. For Z. mays, soil inoculation decreased the accumulation of Cr, Pb, Co, Ge, and REEs (significant for Co with 57%) but showed an insignificant increased uptake of Cu, As, and nutrient elements. Summarily, the results suggest that bioaugmentation with B. amyloliquefaciens is safe and has the potential to enhance/reduce the phytoaccumulation of some elements and the effects of inoculation are plant specific.
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Affiliation(s)
- Precious Uchenna Okoroafor
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
- Correspondence:
| | - Lotte Mann
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Kerian Amin Ngu
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Nazia Zaffar
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Nthati Lillian Monei
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
- Mining Department, Geology Institute, Tallinn University of Technology, 19086 Tallin, Estonia
| | - Christin Boldt
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research–UFZ, Theodor–Lieser Str. 4, 06120 Halle, Germany;
| | - Hermann Heilmeier
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Oliver Wiche
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
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20
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Rico-Jiménez M, Roca A, Krell T, Matilla MA. A bacterial chemoreceptor that mediates chemotaxis to two different plant hormones. Environ Microbiol 2022; 24:3580-3597. [PMID: 35088505 PMCID: PMC9543091 DOI: 10.1111/1462-2920.15920] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Indole-3-acetic acid (IAA) is the main naturally occurring auxin and is produced by organisms of all kingdoms of life. In addition to the regulation of plant growth and development, IAA plays an important role in the interaction between plants and growth-promoting and phytopathogenic bacteria by regulating bacterial gene expression and physiology. We show here that a IAA metabolizing plant-associated Pseudomonas putida isolate exhibits chemotaxis to IAA that is independent of auxin metabolism. We found that IAA chemotaxis is based on the activity of the PcpI chemoreceptor and heterologous expression of pcpI conferred IAA taxis to different environmental and human pathogenic isolates of the Pseudomonas genus. Using ligand screening, microcalorimetry and quantitative chemotaxis assays, we found that PcpI failed to bind IAA directly, but recognized and mediated chemoattractions to various aromatic compounds, including the phytohormone salicylic acid. The expression of pcpI and its role in the interactions with plants was also investigated. PcpI extends the range of central signal molecules recognized by chemoreceptors. To our knowledge, this is the first report on a bacterial receptor that responds to two different phytohormones. Our study reinforces the multifunctional role of IAA and salicylic acid as intra- and inter-kingdom signal molecules. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Miriam Rico-Jiménez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Amalia Roca
- Department of Microbiology, Facultad de Farmacia, Campus Universitario de Cartuja, Universidad de Granada, 18071, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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21
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He T, Xu ZJ, Wang JF, Wang FP, Zhou XF, Wang LL, Li QS. Improving cadmium accumulation by Solanum nigrum L. via regulating rhizobacterial community and metabolic function with phosphate-solubilizing bacteria colonization. CHEMOSPHERE 2022; 287:132209. [PMID: 34826911 DOI: 10.1016/j.chemosphere.2021.132209] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 05/03/2023]
Abstract
Soil cadmium (Cd) mobilized with phosphate-solubilizing bacteria (PSB), especially for strains effectively colonized in rhizosphere, is an important pathway for promoting its accumulation by Cd-hyperaccumulators. In this study, screened PSB strains, Acinetobacter pittii (AP) and Escherichia coli (EC), were used to evaluate their effects on Cd mobilization in rhizosphere, Cd accumulation by Solanum nigrum L., and rhizobacterial community and metabolic function under different colonization condition. Results indicated that AP or EC inoculated in soils significantly promoted plant growth, and simultaneously motivated Cd accumulation in S. nigrum L. by 119% and 88%, respectively, when compared with that of uninoculated treatment. Higher efficiency colonization of AP contributed to more organic acids (malic, l-proline, l-alanine, and γ-aminobutanoic) production in the rhizosphere soil and Cd accumulation by S. nigrum L., when compared with that of EC treatment. Taxonomic distribution and co-occurrence network analyses demonstrated that inoculation of AP or EC enriched dominant microbial taxa with plant growth promotion function and keystone taxa related to Cd mobilization in the rhizosphere soil, respectively. Inoculated strains up-regulated the expression of genes related to bacterial mobility, amino acid metabolism, and carbon metabolism among rhizobacterial community. Overall, this study provided a feasible method for soil Cd phytoremediation by promoting Cd mobilization with the enhancement of keystone taxa and organic acid secretion based on the high-efficiency colonization of PSB.
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Affiliation(s)
- Tao He
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Zi-Jie Xu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Jun-Feng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Fo-Peng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Xue-Fang Zhou
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Li-Li Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Qu-Sheng Li
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China.
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22
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Zhang H, Qian Y, Fan D, Tian Y, Huang X. Biofilm formed by Hansschlegelia zhihuaiae S113 on root surface mitigates the toxicity of bensulfuron-methyl residues to maize. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118366. [PMID: 34653590 DOI: 10.1016/j.envpol.2021.118366] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/20/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Bensulfuron-methyl (BSM) residues in soil threaten the rotation of BSM-sensitive crops. Microbial biofilms formed on crop roots could improve the ability of microbes to survive and protect crop roots. However, the research on biofilms with the purpose of mitigating or even eliminating BSM damage to sensitive crops is very limited. In this study, one BSM-degrading bacterium, Hansschlegelia zhihuaiae S113, colonized maize roots by forming a biofilm. Root exudates were associated with increased BSM degradation efficiency with strain S113 in rhizosphere soil relative to bulk soil, so the interactions among BSM degradation, root exudates, and biofilms may provide a new approach for the BSM-contaminated soil bioremediation. Root exudates and their constituent organic acids, including fumaric acid, tartaric acid, and l-malic acid, enhanced biofilm formation with 13.0-22.2% increases, owing to the regulation of genes encoding proteins responsible for cell motility/chemotaxis (fla/che cluster) and materials metabolism, thus promoting S113 population increases. Additionally, root exudates were also able to induce exopolysaccharide production to promote mature biofilm formation. Complete BSM degradation and healthy maize growth were found in BSM-contaminated rhizosphere soil treated with wild strain S113, compared to that treated with loss-of-function mutants ΔcheA-S113 (89.3%, without biofilm formation ability) and ΔsulE-S113 (22.1%, without degradation ability) or sterile water (10.7%, control). Furthermore, the biofilm mediated by organic acids, such as l-malic acid, exhibited a more favorable effect on BSM degradation and maize growth. These results showed that root exudates and their components (such as organic acids) can induce the biosynthesis of the biofilm to promote BSM degradation, emphasizing the contribution of root biofilm in reducing BSM damage to maize.
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Affiliation(s)
- Hao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, PR China; Innovation Center of Water Security for Water Source Region of Mid-route Project of South-North Water Diversion of Henan Province, Nanyang Normal University, Nanyang, 473061, PR China
| | - Yingying Qian
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Dandan Fan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yanning Tian
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xing Huang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China.
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23
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Lohse M, Haag R, Lippold E, Vetterlein D, Reemtsma T, Lechtenfeld OJ. Direct Imaging of Plant Metabolites in the Rhizosphere Using Laser Desorption Ionization Ultra-High Resolution Mass Spectrometry. FRONTIERS IN PLANT SCIENCE 2021; 12:753812. [PMID: 34925405 PMCID: PMC8678481 DOI: 10.3389/fpls.2021.753812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
The interplay of rhizosphere components such as root exudates, microbes, and minerals results in small-scale gradients of organic molecules in the soil around roots. The current methods for the direct chemical imaging of plant metabolites in the rhizosphere often lack molecular information or require labeling with fluorescent tags or isotopes. Here, we present a novel workflow using laser desorption ionization (LDI) combined with mass spectrometric imaging (MSI) to directly analyze plant metabolites in a complex soil matrix. Undisturbed samples of the roots and the surrounding soil of Zea mays L. plants from either field- or laboratory-scale experiments were embedded and cryosectioned to 100 μm thin sections. The target metabolites were detected with a spatial resolution of 25 μm in the root and the surrounding soil based on accurate masses using ultra-high mass resolution laser desorption ionization Fourier-transform ion cyclotron resonance mass spectrometry (LDI-FT-ICR-MS). Using this workflow, we could determine the rhizosphere gradients of a dihexose (e.g., sucrose) and other plant metabolites (e.g., coumaric acid, vanillic acid). The molecular gradients for the dihexose showed a high abundance of this metabolite in the root and a strong depletion of the signal intensity within 150 μm from the root surface. Analyzing several sections from the same undisturbed soil sample allowed us to follow molecular gradients along the root axis. Benefiting from the ultra-high mass resolution, isotopologues of the dihexose could be readily resolved to enable the detection of stable isotope labels on the compound level. Overall, the direct molecular imaging via LDI-FT-ICR-MS allows for the first time a non-targeted or targeted analysis of plant metabolites in undisturbed soil samples, paving the way to study the turnover of root-derived organic carbon in the rhizosphere with high chemical and spatial resolution.
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Affiliation(s)
- Martin Lohse
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Rebecca Haag
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- Ansbach University of Applied Sciences, Ansbach, Germany
| | - Eva Lippold
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
- Soil Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Thorsten Reemtsma
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
| | - Oliver J. Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- ProVIS – Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
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24
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Rodríguez-Esperón MC, Eastman G, Sandes L, Garabato F, Eastman I, Iriarte A, Fabiano E, Sotelo-Silveira JR, Platero R. Genomics and transcriptomics insights into luteolin effects on the beta-rhizobial strain Cupriavidus necator UYPR2.512. Environ Microbiol 2021; 24:240-264. [PMID: 34811861 DOI: 10.1111/1462-2920.15845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022]
Abstract
Cupriavidus necator UYPR2.512 is a rhizobial strain that belongs to the Beta-subclass of proteobacteria, able to establish successful symbiosis with Mimosoid legumes. The initial steps of rhizobium-legumes symbioses involve the reciprocal recognition by chemical signals, being luteolin one of the molecules involved. However, there is a lack of information on the effect of luteolin in beta-rhizobia. In this work, we used long-read sequencing to complete the genome of UYPR2.512 providing evidence for the existence of four closed circular replicons. We used an RNA-Seq approach to analyse the response of UYPR2.512 to luteolin. One hundred and forty-five genes were differentially expressed, with similar numbers of downregulated and upregulated genes. Most repressed genes were mapped to the main chromosome, while the upregulated genes were overrepresented among pCne512e, containing the symbiotic genes. Induced genes included the nod operon and genes implicated in exopolysaccharides and flagellar biosynthesis. We identified many genes involved in iron, copper and other heavy metals metabolism. Among repressed genes, we identified genes involved in basal carbon and nitrogen metabolism. Our results suggest that in response to luteolin, C. necator strain UYPR2.512 reshapes its metabolism in order to be prepared for the forthcoming symbiotic interaction.
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Affiliation(s)
- M C Rodríguez-Esperón
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - G Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - L Sandes
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - F Garabato
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - I Eastman
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Montevideo, Uruguay
| | - E Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - J R Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - R Platero
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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25
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Coordinated bacterial and plant sulfur metabolism in Enterobacter sp. SA187-induced plant salt stress tolerance. Proc Natl Acad Sci U S A 2021; 118:2107417118. [PMID: 34772809 PMCID: PMC8609655 DOI: 10.1073/pnas.2107417118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 12/22/2022] Open
Abstract
Although plant growth–promoting bacteria (PGPB) enhance the performance of plants, only a few mechanisms have been identified so far. We show that the sulfur metabolisms in both PGPB Enterobacter sp. SA187 and Arabidopsis plants play a key role in plant salt stress tolerance. Salt stress induces a sulfur starvation response in plants that is attenuated by SA187. Arabidopsis sulfur metabolic mutants are hypersensitive to salt stress but can be rescued by SA187. Most plant sulfur metabolism occurs in chloroplasts and is linked to stress-induced accumulation of reactive oxygen species that is suppressed by SA187. This work reveals that plant salt stress tolerance requires the coordinated regulation of the sulfur metabolic pathways in both beneficial microbe and host plant. Enterobacter sp. SA187 is a root endophytic bacterium that maintains growth and yield of plants under abiotic stress conditions. In this work, we compared the metabolic wirings of Arabidopsis and SA187 in the free-living and endophytic interaction states. The interaction of SA187 with Arabidopsis induced massive changes in bacterial gene expression for chemotaxis, flagellar biosynthesis, quorum sensing, and biofilm formation. Besides modification of the bacterial carbon and energy metabolism, various nutrient and metabolite transporters and the entire sulfur pathway were up-regulated. Under salt stress, Arabidopsis resembled plants under sulfate starvation but not when colonized by SA187, which reprogramed the sulfur regulon of Arabidopsis. In accordance, salt hypersensitivity of multiple Arabidopsis sulfur metabolism mutants was partially or completely rescued by SA187 as much as by the addition of sulfate, L-cysteine, or L-methionine. Many components of the sulfur metabolism that are localized in the chloroplast were partially rescued by SA187. Finally, salt-induced accumulation of reactive oxygen species as well as the hypersensitivity of LSU mutants were suppressed by SA187. LSUs encode a central regulator linking sulfur metabolism to chloroplast superoxide dismutase activity. The coordinated regulation of the sulfur metabolic pathways in both the beneficial microorganism and the host plant is required for salt stress tolerance in Arabidopsis and might be a common mechanism utilized by different beneficial microbes to mitigate the harmful effects of different abiotic stresses on plants.
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26
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Surfactin Stimulated by Pectin Molecular Patterns and Root Exudates Acts as a Key Driver of the Bacillus-Plant Mutualistic Interaction. mBio 2021; 12:e0177421. [PMID: 34724831 PMCID: PMC8561381 DOI: 10.1128/mbio.01774-21] [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] [Indexed: 01/24/2023] Open
Abstract
Bacillus velezensis is considered as a model species belonging to the so-called Bacillus subtilis complex that evolved typically to dwell in the soil rhizosphere niche and establish an intimate association with plant roots. This bacterium provides protection to its natural host against diseases and represents one of the most promising biocontrol agents. However, the molecular basis of the cross talk that this bacterium establishes with its natural host has been poorly investigated. We show here that these plant-associated bacteria have evolved a polymer-sensing system to perceive their host and that, in response, they increase the production of the surfactin-type lipopeptide. Furthermore, we demonstrate that surfactin synthesis is favored upon growth on root exudates and that this lipopeptide is a key component used by the bacterium to optimize biofilm formation, motility, and early root colonization. In this specific nutritional context, the bacterium also modulates qualitatively the pattern of surfactin homologues coproduced in planta and forms mainly variants that are the most active at triggering plant immunity. Surfactin represents a shared good as it reinforces the defensive capacity of the host. IMPORTANCE Within the plant-associated microbiome, some bacterial species are of particular interest due to the disease protective effect they provide via direct pathogen suppression and/or stimulation of host immunity. While these biocontrol mechanisms are quite well characterized, we still poorly understand the molecular basis of the cross talk these beneficial bacteria initiate with their host. Here, we show that the model species Bacillus velezensis stimulates the production of the surfactin lipopeptide upon sensing pectin as a cell surface molecular pattern and upon feeding on root exudates. Surfactin favors bacterial rhizosphere fitness on one hand and primes the plant immune system on the other hand. Our data therefore illustrate how both partners use this multifunctional compound as a unique shared good to sustain a mutualistic interaction.
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27
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Aguirre-Noyola JL, Rosenblueth M, Santiago-Martínez MG, Martínez-Romero E. Transcriptomic Responses of Rhizobium phaseoli to Root Exudates Reflect Its Capacity to Colonize Maize and Common Bean in an Intercropping System. Front Microbiol 2021; 12:740818. [PMID: 34777287 PMCID: PMC8581550 DOI: 10.3389/fmicb.2021.740818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022] Open
Abstract
Corn and common bean have been cultivated together in Mesoamerica for thousands of years in an intercropping system called "milpa," where the roots are intermingled, favoring the exchange of their microbiota, including symbionts such as rhizobia. In this work, we studied the genomic expression of Rhizobium phaseoli Ch24-10 (by RNA-seq) after a 2-h treatment in the presence of root exudates of maize and bean grown in monoculture and milpa system under hydroponic conditions. In bean exudates, rhizobial genes for nodulation and degradation of aromatic compounds were induced; while in maize, a response of genes for degradation of mucilage and ferulic acid was observed, as well as those for the transport of sugars, dicarboxylic acids and iron. Ch24-10 transcriptomes in milpa resembled those of beans because they both showed high expression of nodulation genes; some genes that were expressed in corn exudates were also induced by the intercropping system, especially those for the degradation of ferulic acid and pectin. Beans grown in milpa system formed nitrogen-fixing nodules similar to monocultured beans; therefore, the presence of maize did not interfere with Rhizobium-bean symbiosis. Genes for the metabolism of sugars and amino acids, flavonoid and phytoalexin tolerance, and a T3SS were expressed in both monocultures and milpa system, which reveals the adaptive capacity of rhizobia to colonize both legumes and cereals. Transcriptional fusions of the putA gene, which participates in proline metabolism, and of a gene encoding a polygalacturonase were used to validate their participation in plant-microbe interactions. We determined the enzymatic activity of carbonic anhydrase whose gene was also overexpressed in response to root exudates.
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Affiliation(s)
- José Luis Aguirre-Noyola
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mónica Rosenblueth
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Esperanza Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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28
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Sivakumar R, Gunasekaran P, Rajendhran J. Inactivation of CbrAB two-component system hampers root colonization in rhizospheric strain of Pseudomonas aeruginosa PGPR2. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194763. [PMID: 34530138 DOI: 10.1016/j.bbagrm.2021.194763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/24/2022]
Abstract
Two-component systems (TCS) are one of the signal transduction mechanisms, which sense physiological/biological restraints and respond to changing environmental conditions by regulating the gene expression. Previously, by employing a forward genetic screen (INSeq), we identified that cbrA gene is essential for the fitness of Pseudomonas aeruginosa PGPR2 during root colonization. Here, we report the functional characterization of cbrAB TCS in PGPR2 during root colonization. We constructed insertion mutants in cbrA and its cognate response regulator cbrB. Genetic characterization revealed drastic down-regultion of sRNA crcZ gene in both mutant strains which play a critical role in carbon catabolite repression (CCR). The mutant strains displayed 10-fold decreased root colonization efficiency when compared to the wild-type strain. On the other hand, mutant strains formed higher biofilm on the abiotic surface, and the expression of pelB and pslA genes involved in biofilm matrix formation was up-regulated. In contrast, the expression of algD, responsible for alginate production, and its associated sigma factor algU was significantly down-regulated in mutant strains. We further analyzed the transcript levels of rsmA, controlled by the algU sigma factor, and found that the expression of rsmA was hampered in both mutants. The ability of mutant strains to swim and swarm was significantly hindered. Also, the expression of genes associated with type III secretion system (T3SS) was dysregulated in mutant strains. Taken together, regulation of gene expression by CbrAB TCS is intricate, and we confirm its role beyond carbon and nitrogen assimilation.
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Affiliation(s)
- Ramamoorthy Sivakumar
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | | | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India.
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29
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Bargaz A, Elhaissoufi W, Khourchi S, Benmrid B, Borden KA, Rchiad Z. Benefits of phosphate solubilizing bacteria on belowground crop performance for improved crop acquisition of phosphorus. Microbiol Res 2021; 252:126842. [PMID: 34438221 DOI: 10.1016/j.micres.2021.126842] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
Although research on plant growth promoting bacteria began in the 1950s, basic and applied research on bacteria improving use of phosphorus (P) continues to be a priority among many agricultural research institutions. Ultimately, identifying agriculturally beneficial microbes, notably P solubilizing bacteria (PSB), that enhance the efficient use of P supports more sustainable cropping systems and the judicious use of mineral nutrients. In parallel, there is more attention on improving crop root P acquisition of existing soil P pools as well as by increasing the proportion of fertilizer P that is taken up by crops. Today, new lines of research are emerging to investigate the co-optimization of PSB-fertilizer-crop root processes for improved P efficiency and agricultural performance. In this review, we compile and summarize available findings on the beneficial effects of PSB on crop production with a focus on crop P acquisition via root system responses at the structural, functional and transcriptional levels. We discuss the current state of knowledge on the mechanisms of PSB-mediated P availability, both soil- and root-associated, as well as crop uptake via P solubilization, mineralization and mobilization, mainly through the production of organic acids and P-hydrolyzing enzymes, and effects on phytohormone signaling for crop root developement. The systematic changes caused by PSB on crop roots are discussed and contextualized within promising functional trait-based frameworks. We also detail agronomic profitability of P (mineral and organic) and PSB co-application, in amended soils and inoculated crops, establishing the connection between the influence of PSB on agroecosystem production and the impact of P fertilization on microbial diversity and crop functional traits for P acquisition.
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Affiliation(s)
- Adnane Bargaz
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, 43150, Morocco.
| | - Wissal Elhaissoufi
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, 43150, Morocco; Cadi Ayyad University, Faculty of Sciences and Techniques, Biology Dep., Marrakech, Morocco
| | - Said Khourchi
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, 43150, Morocco; University of Liège, Gembloux Agro-Bio Tech, Liège, Belgium
| | - Bouchra Benmrid
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, 43150, Morocco
| | - Kira A Borden
- University of British Columbia, Faculty of Land and Food Systems, Vancouver, V6T 1Z4, Canada
| | - Zineb Rchiad
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, 43150, Morocco
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30
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Wang JF, Li WL, Li QS, Wang LL, He T, Wang FP, Xu ZM. Nitrogen fertilizer management affects remobilization of the immobilized cadmium in soil and its accumulation in crop tissues. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:31640-31652. [PMID: 33609242 DOI: 10.1007/s11356-021-12868-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/05/2021] [Indexed: 05/22/2023]
Abstract
Immobilization of soil cadmium (Cd) has been the strategy mostly used in remediation of Cd-contaminated arable soil. However, Cd might be remobilized after the immobilization process through the acid-soluble and complexation effects. Development of agronomic management technologies to prevent soil Cd remobilization after the immobilization process was an important pathway to control the food safety of agricultural products in soils with the immobilized Cd. In this study, the ammonia (NH4+-N) and nitrate (NO3--N) forms with concentrations of 60, 90, and 150 mg-N kg-1 soil were performed for evaluating their effects on Cd remobilization with planted or unplanted treatments and Cd accumulation in tissues of edible amaranth (Liuye). With an initial soil palygorskite-bound fraction Cd concentration of 0.6 mg kg-1, bioavailable Cd in rhizosphere soils and Cd in crop shoots respectively increased from 11.4 to 20.6 μg kg-1 (dry soil weight) and 6.92 to 14.92 mg kg-1 (dry plant weight) in planted NH4+-N treatments, while significantly lower concentrations of bioavailable Cd in rhizosphere soils and Cd in crop tissues were observed with planted NO3--N treatments. Compared with that of planted NO3--N treatments, decreasing pH value (i.e., 7.64 to 7.18) induced by root proton efflux during the absorption of NH4+-N, enhancive organic/amino acid (oxalic acid, lactic acid, L-proline, and so on) secretion from roots, and increasing abundance of bacteria distributed in phyla Proteobacteria, Cyanobacteria, and Bacteroidetes with Cd mobilization ability in rhizosphere soils were the main reasons found in this study for the higher Cd remobilization in soils and Cd accumulation in crop under NH4+-N treatments. Moreover, the direct effect of NH4+-N on remobilization of immobilized Cd by upregulating the expression abundances of genes associated with pyruvate metabolism and amino acids metabolism was more significant than that of NO3--N. In summary, the use of NO3--N as preferred N fertilizer was more efficient to ensure the food safety of agricultural products than that of NH4+-N in Cd-contaminated arable soil after immobilization process.
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Affiliation(s)
- Jun-Feng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Wan-Li Li
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Qu-Sheng Li
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China.
| | - Li-Li Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Tao He
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Fo-Peng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Zhi-Min Xu
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
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31
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Zheng L, Huang S, Hsiang T, Yu G, Guo D, Jiang Z, Li J. Biocontrol Using Bacillus amyloliquefaciens PP19 Against Litchi Downy Blight Caused by Peronophythora litchii. Front Microbiol 2021; 11:619423. [PMID: 33510732 PMCID: PMC7835641 DOI: 10.3389/fmicb.2020.619423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/08/2020] [Indexed: 11/13/2022] Open
Abstract
Bacillus amyloliquefaciens has been widely used in the agriculture, food, and medicine industries. Isolate PP19 was obtained from the litchi fruit carposphere and showed biocontrol efficacy against litchi downy blight (LDB) whether applied preharvest or postharvest. To further understand the underlying regulatory mechanisms, the genome of PP19 was sequenced and analyzed. The genome comprised a 3,847,565 bp circular chromosome containing 3990 protein-coding genes and 121 RNA genes. It has the smallest genome among 36 sequenced strains of B. amyloliquefaciens except for RD7-7. In whole genome phylogenetic analysis, PP19 was clustered into a group with known industrial applications, indicating that it may also produce high-yield metabolites that have yet to be identified. A large chromosome structural variation and large numbers of single nucleotide polymorphisms (SNPs) between PP19 (industrial strain) and UMAF6639 (plant-associated strain) were detected through comparative analysis, which may shed light on their functional differences. Preharvest treatment with PP19 enhanced resistance to LDB, by decreasing the plant H2O2 content and increasing the SOD activity. This is the first report of an industrial strain of B. amyloliquefaciens showing a plant-associated function and with major potential for the biocontrol of LDB.
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Affiliation(s)
- Li Zheng
- Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Chinese Academy of Tropical Agricultural Sciences Guangzhou Experimental Station, Guangzhou, China
| | - Shilian Huang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratary of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Guohui Yu
- Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Dongliang Guo
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratary of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zide Jiang
- Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Jianguang Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratary of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Sivakumar R, Gunasekaran P, Rajendhran J. Functional characterization of asnC family transcriptional regulator in Pseudomonas aeruginosa PGPR2 during root colonization. Mol Biol Rep 2020; 47:7941-7957. [PMID: 33011891 DOI: 10.1007/s11033-020-05872-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022]
Abstract
Transcriptional regulators in bacteria are the crucial players in mediating communication between environmental cues and DNA transcription through a complex network process. Pseudomonas aeruginosa PGPR2 is an efficient root colonizer and a biocontrol strain. Previously, we identified that the transcriptional regulator, asnC, negatively regulates the corn root colonization of P. aeruginosa PGPR2. In a transposon insertion sequencing (INSeq) screen, the asnC insertion mutant was positively selected during root colonization, meaning the disruption of asnC improves the fitness of the P. aeruginosa PGPR2 strain for the root colonization. In this study, we constructed isogenic mutant of asnC family transcriptional regulator encoded by PGPR2_17510 by allele exchange mutagenesis. The ΔasnC mutant was able to efficiently colonize corn roots with a twofold increase in population when compared to the wild-type strain. Similarly, the mutant strain outcompeted the wild-type strain in a competition assay, where the mutant strain represented 90% of the total population recovered from the root. We compared the whole transcriptome of the wild-type and the ΔasnC mutant of P. aeruginosa PGPR2 when exposed to the corn root exudates. The RNA-Seq revealed that a total of 360 genes were differentially expressed in the ΔasnC strain of P. aeruginosa PGPR2. Inactivation of asnC transcriptional regulator resulted in the up-regulation of several genetic factors implicated in metabolism, uptake of nutrients, motility, stress response, and signal transduction, which could play crucial roles in root colonization. This notion was further validated by phenotypic characterization and quantification of transcription pattern of selected genes associated with metabolism, motility, and carbon catabolite repression between wild type and mutant strain, which was in agreement with transcriptome data. Similarly, ΔasnC strain formed increased biofilm on abiotic surface validating our RNA-seq analysis, where transcript levels of several genes associated with biofilm formation were up-regulated in the mutant strain. We report that the inactivation of an asnC family transcriptional regulator encoded by PGPR2_17510 enhances the root colonization and biofilm-forming ability of P. aeruginosa PGPR2. Together, our results provide evidence for the molecular adaptations that enable ΔasnC mutant strain to colonize on the corn roots and to form a biofilm.
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Affiliation(s)
- Ramamoorthy Sivakumar
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India
| | | | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India.
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Balderas-Ruíz KA, Bustos P, Santamaria RI, González V, Cristiano-Fajardo SA, Barrera-Ortíz S, Mezo-Villalobos M, Aranda-Ocampo S, Guevara-García ÁA, Galindo E, Serrano-Carreón L. Bacillus velezensis 83 a bacterial strain from mango phyllosphere, useful for biological control and plant growth promotion. AMB Express 2020; 10:163. [PMID: 32894363 PMCID: PMC7477031 DOI: 10.1186/s13568-020-01101-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 08/30/2020] [Indexed: 01/05/2023] Open
Abstract
Bacillus velezensis 83 was isolated from mango tree phyllosphere of orchards located in El Rosario, Sinaloa, México. The assessment of this strain as BCA (biological control agent), as well as PGPB (plant growth-promoting bacteria), were demonstrated through in vivo and in vitro assays. In vivo assays showed that B. velezensis 83 was able to control anthracnose (Kent mangoes) as efficiently as chemical treatment with Captan 50 PH™ or Cupravit hidro™. The inoculation of B. velezensis 83 to the roots of maize seedlings yielded an increase of 12% in height and 45% of root biomass, as compared with uninoculated seedlings. In vitro co-culture assays showed that B. velezensis 83 promoted Arabidopsis thaliana growth (root and shoot biomass) while, under the same experimental conditions, B. velezensis FZB42 (reference strain) had a suppressive effect on plant growth. In order to characterize the isolated strain, the complete genome sequence of B. velezensis 83 is reported. Its circular genome consists of 3,997,902 bp coding to 3949 predicted genes. The assembly and annotation of this genome revealed gene clusters related with plant-bacteria interaction and sporulation, as well as ten secondary metabolites biosynthetic gene clusters implicated in the biological control of phytopathogens. Despite the high genomic identity (> 98%) between B. velezensis 83 and B. velezensis FZB42, they are phenotypically different. Indeed, in vitro production of compounds such as surfactin and bacillomycin D (biocontrol activity) and γ-PGA (biofilm component) is significantly different between both strains. ![]()
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Xu Z, Wang D, Tang W, Wang L, Li Q, Lu Z, Liu H, Zhong Y, He T, Guo S. Phytoremediation of cadmium-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization in the Solanum nigrum L. rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 732:139265. [PMID: 32416401 DOI: 10.1016/j.scitotenv.2020.139265] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/23/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Microbe-assisted phytoremediation for Cd-polluted soil is being regarded increasingly. However, the availability of microbes that can collaborate with Cd-hyperaccumulators effectively has become one of bottlenecks restricting the remediation efficiency. A siderophore-producing bacterium (Y16; Enterobacter cloacae) isolated from the rhizospheric soil of Cd-hyperaccumulator Solanum nigrum L. was identified by 16S rRNA gene sequencing and biochemical analysis, and then used for analyzing microbial chemotaxis, carbon source utilization, and insoluble P/Cd mobilization capacities. Besides, a soil-pot trial was performed to underlie the phytoremediation mechanism of Cd-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization (DEYC) in the Solanum nigrum L. rhizosphere. Results displayed that D-gluconate was an effective chemoattractant and carbon source strengthening Y16 colonization, and Y16 exhibited strong abilities to mobilize insoluble P/Cd in shake flask by extracellular acidification (p < 0.05). In the soil-pot trial, DEYC observably enhanced soil Cd phytoextraction by Solanum nigrum L., and increased microbial diversity according to alpha- and beta-diversity analysis (p < 0.05). Taxonomic distribution and co-occurrence network analysis suggested that DEYC increased relative abundances of dominant microbial taxa associated with soil acidification (Acidobacteria-6), indoleacetic acid secretion (Ensifer adhaerens), soil fertility improvement (Flavisolibacter, Bdellovibrio bacteriovorus, and Candidatus nitrososphaera), and insoluble Cd mobilization (Massilia timonae) at different classification levels. Importantly, COGs analysis further shown that DEYC aroused the up-regulation of key genes related to chemotactic motility, carbon fixation, TCA cycle, and propanoate metabolism. These results indicated that DEYC drove the rhizospheric enrichment of pivotal microbial taxa directly or indirectly involved in soil Cd mobilization, meanwhile distinctly promoted plant growth for accumulating more mobilizable Cd. Therefore, Y16 could be used as bio-inoculants for assisting phytoremediation of Cd-polluted soil.
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Affiliation(s)
- Zhimin Xu
- School of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China; Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, Guangzhou 510225, China
| | - Dongsheng Wang
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Wanpeng Tang
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Lili Wang
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Qusheng Li
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ziyan Lu
- School of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, Guangzhou 510225, China
| | - Hui Liu
- School of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, Guangzhou 510225, China
| | - Yuming Zhong
- School of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, Guangzhou 510225, China
| | - Tao He
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Shihong Guo
- Fujian Provincial Academy of Environmental Science, Fuzhou 350013, China
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Mirghasempour A, Glick BR, Hou Y, Huang S. A system to study the expression of phytopathogenic genes encoded by Burkholderia glumae. Arch Microbiol 2020; 203:383-387. [PMID: 32785734 DOI: 10.1007/s00203-020-01986-w] [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: 10/31/2019] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 11/28/2022]
Abstract
Rice is often infected by bacterial panicle blight disease caused by Burkholderia glumae. Since most studies have assessed the transcriptome of the plant when it is exposed to bacteria, the gene expression of the phytopathogenic bacteria have not been well elaborated during the infection process or in the host cell. Recently, a few researches were conducted to evaluate the in vivo transcriptome of bacteria during the infective process. Most bacterial cells do not express genes involved in pathogenicity in culture medium making it difficult to investigate gene expression of bacterial cells in plant cells. Here, we sought a simulated patho-system that would allow bacterial cells to express their pathogenic genes. Thus, rice root exudates (RE) and bacterial N-acyl homoserine lactone (AHL) were used and their effects on bacterial gene expression were assessed. Transcription patterns of B. glumae virulence determinants showed that enrichment medium (LB + RE + C8-HSL) could significantly induce virulence factor genes compared with Luria Bertani (LB; control) medium. The data indicate that the artificial environment is similar to the real patho-system, and that this induced maximum relevant gene expression. In this model system, bacterial gene expression changes are traceable in the infection process. Bacterial cells exposed to either an artificial environment or LB + RE + C8-HSL behaved similarly to the natural environment in situ.
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Affiliation(s)
- A Mirghasempour
- China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - B R Glick
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Y Hou
- China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - S Huang
- China National Rice Research Institute, Hangzhou, 310006, People's Republic of China.
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Lin CH, Lu CY, Tseng AT, Huang CJ, Lin YJ, Chen CY. The ptsG Gene Encoding the Major Glucose Transporter of Bacillus cereus C1L Participates in Root Colonization and Beneficial Metabolite Production to Induce Plant Systemic Disease Resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:256-271. [PMID: 31809253 DOI: 10.1094/mpmi-06-19-0165-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rhizosphere interactions between microorganisms and plants have great influence on plant health. Bacillus cereus C1L, an induced systemic resistance (ISR)-eliciting rhizobacterium from Lilium formosanum, can protect monocot and dicot plants from disease challenges. To identify the ISR-involved bacterial genes, the systemic protection effect of transposon-tagged mutants of B. cereus C1L against southern corn leaf blight (SCLB) was surveyed, and a mutant of the ptsG gene encoding glucose-specific permease of the phosphotransferase system was severely impaired in the abilities of disease suppression and root colonization. The ptsG mutant lost the preferential utilization of glucose and showed reduction of glucose-assisted growth in minimal medium. A promoter-based reporter assay revealed that ptsG expression could be activated by certain sugar constituents of maize root exudates, among which B. cereus C1L exhibited the highest chemotactic response toward glucose, whereas neither of them could attract the ptsG mutant. Additionally, ptsG deficiency almost completely abolished glucose uptake of B. cereus C1L. Metabolite analysis indicated that the lack of ptsG undermined glucose-induced accumulation of acetoin and 2,3-butanediol in B. cereus C1L, both eliciting maize ISR against SCLB. Pretreatments with B. cereus C1L, ptsG mutant, acetoin, and 2,3-butanediol enhanced defense-related reactive oxygen species accumulation and callose deposition at different levels that were positively correlated to their ISR-eliciting activities. Thus, glucose uptake-mediating ptsG participates in ISR elicitation by endowing B. cereus C1L with the full capacities for root colonization and beneficial glucose metabolite production, providing a clue regarding how ISR-mediating rhizobacteria create a mutually beneficial relationship with various plant species.
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Affiliation(s)
- Chia-Hua Lin
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Yen Lu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan
| | - Ann-Tze Tseng
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Jui Huang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan
- Department of Plant Medicine, National Chiayi University, Chiayi 60004, Taiwan
| | - Yu-Ju Lin
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan
| | - Chao-Ying Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan
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Fan B, Wang C, Ding X, Zhu B, Song X, Borriss R. AmyloWiki: an integrated database for Bacillus velezensis FZB42, the model strain for plant growth-promoting Bacilli. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5520604. [PMID: 31219564 PMCID: PMC6585148 DOI: 10.1093/database/baz071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/27/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022]
Abstract
Since its isolation 20 years ago, many studies have been devoted to Bacillus velezensis FZB42 (former name Bacillus amyloliquefaciens subsp. plantarum FZB42), which has been gradually accepted as a model organism for Gram-positive rhizobacteria. FZB42 is different from another widely studied bacterial strain, Bacillus subtilis 168, in its many features that are closely associated with plants. FZB42 represents a large group of Bacillus isolates that are beneficial to plants and of great importance in agriculture. In this work a database for FZB42 named 'AmyloWiki' is built to integrate all information of FZB42 available to date. The information includes the genomic, transcriptomic, proteomic, post-translational data as well as FZB42 unique genes, protein regulators, mutant availability, publications and etc. The website is built up with PHP and MySQL with a function of keyword searching, browsing, data-downloading and other functions.
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Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Cong Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Xiaolei Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Bingyao Zhu
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, 10115 Berlin, Germany, and Nord Reet UG, Marienstr. 27a, 17489 Greifswald, Germany
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Reva ON, Swanevelder DZH, Mwita LA, Mwakilili AD, Muzondiwa D, Joubert M, Chan WY, Lutz S, Ahrens CH, Avdeeva LV, Kharkhota MA, Tibuhwa D, Lyantagaye S, Vater J, Borriss R, Meijer J. Genetic, Epigenetic and Phenotypic Diversity of Four Bacillus velezensis Strains Used for Plant Protection or as Probiotics. Front Microbiol 2019; 10:2610. [PMID: 31803155 PMCID: PMC6873887 DOI: 10.3389/fmicb.2019.02610] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Bacillus velezensis strains are applied as ecologically safe biopesticides, plant growth promoting rhizobacteria (PGPR), and in veterinary probiotics. They are abundant in various environments including soil, plants, marine habitats, the intestinal micro-flora, etc. The mechanisms underlying this adaptive plasticity and bioactivity are not well understood, nor is it clear why several strains outperform other same species isolates by their bioactivities. The main objective of this work was to demonstrate versatility of bioactivities and lifestyle strategies of the selected B. velezensis strains suitable to serve as model organisms in future studies. Here, we performed a comparative study of newly sequenced genomes of four B. velezensis isolates with distinct phenotypes and isolation origin, which were assessed by RNA sequencing under the effect of root exudate stimuli and profiled by epigenetic modifications of chromosomal DNA. Among the selected strains, UCMB5044 is an oligotrophic PGPR strain adapted to nutrient poor desert soils. UCMB5113 and At1 are endophytes that colonize plants and require nutrient rich media. In contrast, the probiotic strain, UCMB5007, is a copiotroph, which shows no propensity to colonize plants. PacBio and Illumina sequencing approaches were used to generate complete genome assemblies, tracing epigenetic modifications, and determine gene expression profiles. All sequence data was deposited at NCBI. The strains, UCMB5113 and At1, show 99% sequence identity and similar phenotypes despite being isolated from geographically distant regions. UCMB5007 and UCMB5044 represent another group of organisms with almost identical genomes but dissimilar phenotypes and plant colonization propensity. The two plant associated strains, UCMB5044 and UCMB5113, share 398 genes putatively associated with root colonization, which are activated by exposure to maize root exudates. In contrast, UCMB5007 did not respond to root exudate stimuli. It was hypothesized that alterations in the global methylation pattern and some other epigenetic modifications enable adaptation of strains to different habitats and therefore may be of importance in terms of the biotechnological applicability of these bacteria. Contrary, the ability to grow on root exudates as a sole source of nutrients or a strong antagonism against phytopathogens showed by the strains in vitro cannot be considered as good predictors of PGPR activities.
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Affiliation(s)
- Oleg N Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Liberata A Mwita
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.,Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Aneth David Mwakilili
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania.,Department of Plant Protection, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Dillon Muzondiwa
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Monique Joubert
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Wai Yin Chan
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.,Forestry and Agricultural Biotechnology Institute, DST-NRF Centre of Excellence in Tree Health Biotechnology, University of Pretoria, Pretoria, South Africa
| | - Stefanie Lutz
- Agroscope, Molecular Diagnostics, Genomics and Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics and Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Lylia V Avdeeva
- Department of Antibiotics, D.K. Zabolotny Institute of Microbiology and Virology, Kyiv, Ukraine
| | - Maksim A Kharkhota
- Department of Antibiotics, D.K. Zabolotny Institute of Microbiology and Virology, Kyiv, Ukraine
| | - Donatha Tibuhwa
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Sylvester Lyantagaye
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | | | - Rainer Borriss
- Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Johan Meijer
- Department of Plant Biology, Linnéan Center for Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Rolfe SA, Griffiths J, Ton J. Crying out for help with root exudates: adaptive mechanisms by which stressed plants assemble health-promoting soil microbiomes. Curr Opin Microbiol 2019; 49:73-82. [PMID: 31731229 DOI: 10.1016/j.mib.2019.10.003] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/29/2019] [Accepted: 10/03/2019] [Indexed: 01/13/2023]
Abstract
Plants employ immunological and ecological strategies to resist biotic stress. Recent evidence suggests that plants adapt to biotic stress by changing their root exudation chemistry to assemble health-promoting microbiomes. This so-called 'cry-for-help' hypothesis provides a mechanistic explanation for previously characterized soil feedback responses to plant disease, such as the development of disease-suppressing soils upon successive cultivations of take all-infected wheat. Here, we divide the hypothesis into individual stages and evaluate the evidence for each component. We review how plant immune responses modify root exudation chemistry, as well as what impact this has on microbial activities, and the subsequent plant responses to these activities. Finally, we review the ecological relevance of the interaction, along with its translational potential for future crop protection strategies.
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Affiliation(s)
- Stephen A Rolfe
- Plant Production and Protection (P(3)), Institute for Sustainable Food, The University of Sheffield, S10 2TN, UK; Department of Animal and Plant Sciences, The University of Sheffield, S10 2TN, UK
| | - Joseph Griffiths
- Department of Animal and Plant Sciences, The University of Sheffield, S10 2TN, UK
| | - Jurriaan Ton
- Plant Production and Protection (P(3)), Institute for Sustainable Food, The University of Sheffield, S10 2TN, UK; Department of Animal and Plant Sciences, The University of Sheffield, S10 2TN, UK.
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Selection of reference genes for measuring the expression of aiiO in Ochrobactrum quorumnocens A44 using RT-qPCR. Sci Rep 2019; 9:13129. [PMID: 31511547 PMCID: PMC6739375 DOI: 10.1038/s41598-019-49474-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/22/2019] [Indexed: 11/09/2022] Open
Abstract
Reverse transcription quantitative PCR (RT-qPCR), a method of choice for quantification of gene expression changes, requires stably expressed reference genes for normalization of data. So far, no reference genes were established for the Alphaproteobacteria of the genus Ochrobactrum. Here, we determined reference genes for gene expression studies in O. quorumnocens A44. Strain A44 was cultured under 10 different conditions and the stability of expression of 11 candidate genes was evaluated using geNorm, NormFinder and BestKeeper. Most stably expressed genes were found to be rho, gyrB and rpoD. Our results can facilitate the choice of reference genes in the related Ochrobactrum strains. O. quorumnocens A44 is able to inactivate a broad spectrum of N-acyl homoserine lactones (AHLs) - the quorum sensing molecules of many Gram-negative bacteria. This activity is attributed to AiiO hydrolase, yet it remains unclear whether AHLs are the primary substrate of this enzyme. Using the established RT-qPCR setup, we found that the expression of the aiiO gene upon exposure to two AHLs, C6-HLS and 3OC12-HSL, does not change above the 1-fold significance threshold. The implications of this finding are discussed in the light of the role of quorum sensing-interfering enzymes in the host strains.
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Gómez-Godínez LJ, Fernandez-Valverde SL, Martinez Romero JC, Martínez-Romero E. Metatranscriptomics and nitrogen fixation from the rhizoplane of maize plantlets inoculated with a group of PGPRs. Syst Appl Microbiol 2019; 42:517-525. [DOI: 10.1016/j.syapm.2019.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 10/26/2022]
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Samain E, Aussenac T, Selim S. The Effect of Plant Genotype, Growth Stage, and Mycosphaerella graminicola Strains on the Efficiency and Durability of Wheat-Induced Resistance by Paenibacillus sp. Strain B2. FRONTIERS IN PLANT SCIENCE 2019; 10:587. [PMID: 31143198 PMCID: PMC6521617 DOI: 10.3389/fpls.2019.00587] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/18/2019] [Indexed: 05/20/2023]
Abstract
Plant-growth-promoting rhizobacteria are known as potential biofertilizers and plant-resistance inducers. The current work aims to study the durability of the resistance induced as a response to the inoculation of wheat grains with Paenibacillus sp. strain B2 (PB2) and its influence by plant genotype, growth stage, and Mycosphaerella graminicola strain (the causal agent of Septoria tritici blotch or STB). The results of the plate-counting method showed that PB2 has high potential for wheat-root external colonization [>106 colony-forming unit (CFU)/g of root], and the quantitative real-time polymerase chain reaction (qPCR) analysis demonstrated its internal root-colonization capacity on all tested cultivars. However, the colonization seems to be dependent on wheat-growth stage. The durability of PB2-induced resistance (PB2-IR) was tested at the 3-leaf, tillering, and flag-leaf-growth stages. Additionally, the results showed that the PB2-IR is durable and able to protect the flag leaf, the most important leaf layer during grain fill. It conferred a high protection efficiency (55-94%) against four virulent strains of M. graminicola and over 11 wheat cultivars with different resistance levels to STB. Although, PB2-IR is dependent on M. graminicola strains, wheat genotypes and growth stages, its efficiency, under field conditions, at protecting the last wheat-leaf layers was not an influence. However, it showed 71-79% of protection and reached 81-94% in association with half of the recommended dose of Cherokee® fungicide. This may be explained using laboratory results by its direct impact on M. graminicola strains in these leaf layers and by the indirect reduction of the inoculum coming from leaves infected during the earlier growth stages. Gene expression results showed that PB2-IR is correlated to upregulation of genes involved in defense and cell rescue and a priming effect in the basal defense, jasmonic acid signaling, phenylpropanoids and phytoalexins, and reactive oxygen species gene markers. To conclude, PB2 induces a high and durable resistance against M. graminicola under controlled and field conditions. The PB2-IR is a pathogen strain and is plant-growth-stage and genotype dependent. These results highlight the importance of taking into consideration these factors so as to avoid losing the effectiveness of induced resistance under field conditions.
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Affiliation(s)
- Erika Samain
- AGHYLE, College of Agricultural Sciences, Institut Polytechnique UniLaSalle, Beauvais, France
- SDP, Laon, France
| | - Thierry Aussenac
- UP Transformations & Agro-Ressources, Institut Polytechnique UniLaSalle, Beauvais, France
| | - Sameh Selim
- AGHYLE, College of Agricultural Sciences, Institut Polytechnique UniLaSalle, Beauvais, France
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Jin Y, Zhu H, Luo S, Yang W, Zhang L, Li S, Jin Q, Cao Q, Sun S, Xiao M. Role of Maize Root Exudates in Promotion of Colonization of Bacillus velezensis Strain S3-1 in Rhizosphere Soil and Root Tissue. Curr Microbiol 2019; 76:855-862. [PMID: 31073734 DOI: 10.1007/s00284-019-01699-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/29/2019] [Indexed: 01/09/2023]
Abstract
Bacillus velezensis strain S3-1 has a broad range of hosts and is used as a biocontrol agent and biofertilizer. However, the interaction of maize root exudates and colonization of the strain S3-1 has not yet been investigated. In our study, strain S3-1 effectively colonized both rhizosphere soil and root tissue. Collected maize root exudates significantly induced the chemotaxis, cluster movement, and biofilm formation of strain S3-1, showing increases of 1.43, 1.6, and 2.08 times, respectively, compared with the control. In addition, the components of root exudates (organic acids: citric acid, malic acid, and oxalic acid; amino acids: glycine, proline and phenylalanine; sugars: glucose, fructose, and sucrose) were tested. Each of these compounds could induce chemotactic response, swarming motility, and biofilm formation significantly. The strongest chemotactic response and swarming motility were found when malic acid was applied, but maximal ability of biofilm formation was stimulated by proline. Furthermore, we found that these compounds of root exudates stimulated the population of S3-1 adhering to the maize root surface, especially in the presence of malic acid. These results indicate that maize root exudates play an important role in the colonization of S3-1, and provide a deeper understanding of the interaction between plants and microorganisms.
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Affiliation(s)
- Yeqing Jin
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Hangfei Zhu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Si Luo
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Wenwu Yang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Li Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Shanshan Li
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Qing Jin
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Qin Cao
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Shurong Sun
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Ming Xiao
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China.
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López-Farfán D, Reyes-Darias JA, Matilla MA, Krell T. Concentration Dependent Effect of Plant Root Exudates on the Chemosensory Systems of Pseudomonas putida KT2440. Front Microbiol 2019; 10:78. [PMID: 30761113 PMCID: PMC6363813 DOI: 10.3389/fmicb.2019.00078] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/15/2019] [Indexed: 12/28/2022] Open
Abstract
Plant root colonization by rhizobacteria can protect plants against pathogens and promote plant growth, and chemotaxis to root exudates was shown to be an essential prerequisite for efficient root colonization. Since many chemoattractants control the transcript levels of their cognate chemoreceptor genes, we have studied here the transcript levels of the 27 Pseudomonas putida KT2440 chemoreceptor genes in the presence of different maize root exudate (MRE) concentrations. Transcript levels were increased for 10 chemoreceptor genes at low MRE concentrations, whereas almost all receptor genes showed lower transcript levels at high MRE concentrations. The exposure of KT2440 to different MRE concentrations did not alter c-di-GMP levels, indicating that changes in chemoreceptor transcripts are not mediated by this second messenger. Data suggest that rhizosphere colonization unfolds in a temporal fashion. Whereas at a distance to the root, exudates enhance chemoreceptor gene transcript levels promoting in turn chemotaxis, this process is reversed in root vicinity, where the necessity of chemotaxis toward the root may be less important. Insight into KT2440 signaling processes were obtained by analyzing mutants defective in the three cheA paralogous genes. Whereas a mutant in cheA1 showed reduced c-di-GMP levels and impaired biofilm formation, a cheA2 mutant was entirely deficient in MRE chemotaxis, indicating the existence of homologs of the P. aeruginosawsp and che (chemotaxis) pathways. Signaling through both pathways was important for efficient maize root colonization. Future studies will show whether the MRE concentration dependent effect on chemoreceptor gene transcript levels is a feature shared by other species.
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Affiliation(s)
- Diana López-Farfán
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José A Reyes-Darias
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A Matilla
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Ankati S, Rani TS, Podile AR. Partner-triggered proteome changes in the cell wall of Bacillus sonorensis and roots of groundnut benefit each other. Microbiol Res 2018; 217:91-100. [DOI: 10.1016/j.micres.2018.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/02/2018] [Accepted: 10/06/2018] [Indexed: 01/01/2023]
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Fan B, Wang C, Song X, Ding X, Wu L, Wu H, Gao X, Borriss R. Bacillus velezensis FZB42 in 2018: The Gram-Positive Model Strain for Plant Growth Promotion and Biocontrol. Front Microbiol 2018; 9:2491. [PMID: 30386322 PMCID: PMC6198173 DOI: 10.3389/fmicb.2018.02491] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/28/2018] [Indexed: 12/31/2022] Open
Abstract
Bacillus velezensis FZB42, the model strain for Gram-positive plant-growth-promoting and biocontrol rhizobacteria, has been isolated in 1998 and sequenced in 2007. In order to celebrate these anniversaries, we summarize here the recent knowledge about FZB42. In last 20 years, more than 140 articles devoted to FZB42 have been published. At first, research was mainly focused on antimicrobial compounds, apparently responsible for biocontrol effects against plant pathogens, recent research is increasingly directed to expression of genes involved in bacteria–plant interaction, regulatory small RNAs (sRNAs), and on modification of enzymes involved in synthesis of antimicrobial compounds by processes such as acetylation and malonylation. Till now, 13 gene clusters involved in non-ribosomal and ribosomal synthesis of secondary metabolites with putative antimicrobial action have been identified within the genome of FZB42. These gene clusters cover around 10% of the whole genome. Antimicrobial compounds suppress not only growth of plant pathogenic bacteria and fungi, but could also stimulate induced systemic resistance (ISR) in plants. It has been found that besides secondary metabolites also volatile organic compounds are involved in the biocontrol effect exerted by FZB42 under biotic (plant pathogens) and abiotic stress conditions. In order to facilitate easy access to the genomic data, we have established an integrating data bank ‘AmyloWiki’ containing accumulated information about the genes present in FZB42, available mutant strains, and other aspects of FZB42 research, which is structured similar as the famous SubtiWiki data bank.
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Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Cong Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Xiaolei Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liming Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, Berlin, Germany.,Nord Reet UG, Greifswald, Germany
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Al-Ali A, Deravel J, Krier F, Béchet M, Ongena M, Jacques P. Biofilm formation is determinant in tomato rhizosphere colonization by Bacillus velezensis FZB42. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29910-29920. [PMID: 29063401 DOI: 10.1007/s11356-017-0469-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
In this work, the behavior in tomato rhizosphere of Bacillus velezensis FZB42 was analyzed taking into account the surfactin production, the use of tomato roots exudate as substrates, and the biofilm formation. B. velezensis FZB42 and B. amyloliquefaciens S499 have a similar capability to colonize tomato rhizosphere. Little difference in this colonization was observed with surfactin non producing B. velezensis FZB42 mutant strains. B. velezensis is able to grow in the presence of root exudate and used preferentially sucrose, maltose, glutamic, and malic acids as carbon sources. A mutant enable to produce exopolysaccharide (EPS-) was constructed to demonstrate the main importance of biofilm formation on rhizosphere colonization. This mutant had completely lost its ability to form biofilm whatever the substrate present in the culture medium and was unable to efficiently colonize tomato rhizosphere.
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Affiliation(s)
- Ameen Al-Ali
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
- College of Agriculture-Soil, Water and Environmental Research Department, Al-Qasim Green University, Babylon, Iraq
| | - Jovana Deravel
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
| | - François Krier
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France.
| | - Max Béchet
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
| | - Marc Ongena
- Terra Teaching and Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liege, B 5030, Gembloux, Belgium
| | - Philippe Jacques
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
- Terra Teaching and Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liege, B 5030, Gembloux, Belgium
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Mastronardi E, Monreal C, DeRosa MC. Personalized Medicine for Crops? Opportunities for the Application of Molecular Recognition in Agriculture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6457-6461. [PMID: 28985063 DOI: 10.1021/acs.jafc.7b03295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This perspective examines the detection of rhizosphere biomarkers, namely, root exudates and microbial metabolites, using molecular recognition elements, such as molecularly imprinted polymers, antibodies, and aptamers. Tracking these compounds in the rhizosphere could provide valuable insight into the status of the crop and soil in a highly localized way. The outlook and potential impact of the combination of molecular recognition and other innovations, such as nanotechnology and precision agriculture, and the comparison to advances in personalized medicine are considered.
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Affiliation(s)
- Emily Mastronardi
- Department of Chemistry , Carleton University , 1125 Colonel By Drive , Ottawa , Ontario K1S 5B6 , Canada
| | - Carlos Monreal
- Agriculture and Agrifood Canada , 960 Carling Avenue , Neatby Building, Ottawa , Ontario K1Y 4X2 , Canada
| | - Maria C DeRosa
- Department of Chemistry , Carleton University , 1125 Colonel By Drive , Ottawa , Ontario K1S 5B6 , Canada
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Yi Y, Li Z, Kuipers OP. Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates. J Vis Exp 2018. [PMID: 30010657 DOI: 10.3791/57606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Beneficial plant-associated bacteria play an important role in promoting growth and preventing disease in plants. The application of plant growth-promoting rhizobacteria (PGPR) as biofertilizers or biocontrol agents has become an effective alternative to the use of conventional fertilizers and can increase crop productivity at low cost. Plant-microbe interactions depend upon host plant-secreted signals and a reaction hereon by their associated bacteria. However, the molecular mechanisms of how beneficial bacteria respond to their associated plant-derived signals are not fully understood. Assessing the transcriptomic response of bacteria to root exudates is a powerful approach to determine the bacterial gene expression and regulation under rhizospheric conditions. Such knowledge is necessary to understand the underlying mechanisms involved in plant-microbe interactions. This paper describes a detailed protocol to study the transcriptomic response of B. mycoides EC18, a strain isolated from the potato endosphere, to potato root exudates. With the help of recent high-throughput sequencing technology, this protocol can be performed in several weeks and produce massive datasets. First, we collect the root exudates under sterile conditions, after which they are added to B. mycoides cultures. The RNA from these cultures is isolated using a phenol/chloroform method combined with a commercial kit and subjected to quality control by an automated electrophoresis instrument. After sequencing, data analysis is performed with the web-based T-REx pipeline and a group of differentially expressed genes is identified. This method is a useful tool to facilitate new discoveries on the bacterial genes involved in plant-microbe interactions.
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Affiliation(s)
- Yanglei Yi
- Department of Molecular Genetics, University of Groningen
| | - Zhibo Li
- Department of Molecular Genetics, University of Groningen
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