1
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Qi M, Berry JC, Veley KM, O'Connor L, Finkel OM, Salas-González I, Kuhs M, Jupe J, Holcomb E, Glavina Del Rio T, Creech C, Liu P, Tringe SG, Dangl JL, Schachtman DP, Bart RS. Correction: Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. ISME J 2023:10.1038/s41396-023-01442-9. [PMID: 37322286 DOI: 10.1038/s41396-023-01442-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Mingsheng Qi
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Kira M Veley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Lily O'Connor
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Washington University, St. Louis, MO, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Molly Kuhs
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Emily Holcomb
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Cody Creech
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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2
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González-García MP, Conesa CM, Lozano-Enguita A, Baca-González V, Simancas B, Navarro-Neila S, Sánchez-Bermúdez M, Salas-González I, Caro E, Castrillo G, Del Pozo JC. Temperature changes in the root ecosystem affect plant functionality. Plant Commun 2023; 4:100514. [PMID: 36585788 DOI: 10.1016/j.xplc.2022.100514] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 05/11/2023]
Abstract
Climate change is increasing the frequency of extreme heat events that aggravate its negative impact on plant development and agricultural yield. Most experiments designed to study plant adaption to heat stress apply homogeneous high temperatures to both shoot and root. However, this treatment does not mimic the conditions in natural fields, where roots grow in a dark environment with a descending temperature gradient. Excessively high temperatures severely decrease cell division in the root meristem, compromising root growth, while increasing the division of quiescent center cells, likely in an attempt to maintain the stem cell niche under such harsh conditions. Here, we engineered the TGRooZ, a device that generates a temperature gradient for in vitro or greenhouse growth assays. The root systems of plants exposed to high shoot temperatures but cultivated in the TGRooZ grow efficiently and maintain their functionality to sustain proper shoot growth and development. Furthermore, gene expression and rhizosphere or root microbiome composition are significantly less affected in TGRooZ-grown roots than in high-temperature-grown roots, correlating with higher root functionality. Our data indicate that use of the TGRooZ in heat-stress studies can improve our knowledge of plant response to high temperatures, demonstrating its applicability from laboratory studies to the field.
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Affiliation(s)
- Mary Paz González-García
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Carlos M Conesa
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Alberto Lozano-Enguita
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Victoria Baca-González
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Bárbara Simancas
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - María Sánchez-Bermúdez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Isai Salas-González
- Undergraduate Program in Genomic Sciences, Center for Genomics Sciences, Universidad Nacional Autonóma de México, Av. Universidad s/n. Col. Chamilpa, Cuernavaca 62210, Morelos, México
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Gabriel Castrillo
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Juan C Del Pozo
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain.
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3
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Gonin M, Salas-González I, Gopaulchan D, Frene JP, Roden S, Van de Poel B, Salt DE, Castrillo G. Plant microbiota controls an alternative root branching regulatory mechanism in plants. Proc Natl Acad Sci U S A 2023; 120:e2301054120. [PMID: 37011213 PMCID: PMC10104509 DOI: 10.1073/pnas.2301054120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
The establishment of beneficial interactions with microbes has helped plants to modulate root branching plasticity in response to environmental cues. However, how the plant microbiota harmonizes with plant roots to control their branching is unknown. Here, we show that the plant microbiota influences root branching in the model plant Arabidopsis thaliana. We define that the microbiota's ability to control some stages in root branching can be independent of the phytohormone auxin that directs lateral root development under axenic conditions. In addition, we revealed a microbiota-driven mechanism controlling lateral root development that requires the induction of ethylene response pathways. We show that the microbial effects on root branching can be relevant for plant responses to environmental stresses. Thus, we discovered a microbiota-driven regulatory pathway controlling root branching plasticity that could contribute to plant adaptation to different ecosystems.
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Affiliation(s)
- Mathieu Gonin
- School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom
| | - Isai Salas-González
- Center for Genomics Sciences, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - David Gopaulchan
- School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom
| | - Juan P Frene
- School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom
- Future Food Beacon of Excellence, University of Nottingham, LE12 5RD, United Kingdom
| | - Stijn Roden
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Bram Van de Poel
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
- Leuven Plant Institute, KU Leuven, 3001 Leuven, Belgium
| | - David E Salt
- School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom
- Future Food Beacon of Excellence, University of Nottingham, LE12 5RD, United Kingdom
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, LE12 5RD, United Kingdom
- Future Food Beacon of Excellence, University of Nottingham, LE12 5RD, United Kingdom
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4
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Conway JM, Walton WG, Salas-González I, Law TF, Lindberg CA, Crook LE, Kosina SM, Fitzpatrick CR, Lietzan AD, Northen TR, Jones CD, Finkel OM, Redinbo MR, Dangl JL. Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome. Nat Microbiol 2022; 7:1817-1833. [PMID: 36266335 PMCID: PMC9613470 DOI: 10.1038/s41564-022-01244-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 09/02/2022] [Indexed: 11/13/2022]
Abstract
Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon's MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac-like and iad-like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad-like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad-like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
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Affiliation(s)
- Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Theresa F Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chloe A Lindberg
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura E Crook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam D Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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5
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Qi M, Berry JC, Veley KW, O'Connor L, Finkel OM, Salas-González I, Kuhs M, Jupe J, Holcomb E, Glavina Del Rio T, Creech C, Liu P, Tringe SG, Dangl JL, Schachtman DP, Bart RS. Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. ISME J 2022; 16:1957-1969. [PMID: 35523959 PMCID: PMC9296637 DOI: 10.1038/s41396-022-01245-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022]
Abstract
Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.
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Affiliation(s)
- Mingsheng Qi
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Kira W Veley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Lily O'Connor
- Donald Danforth Plant Science Center, St. Louis, MO, USA.,Washington University, St. Louis, MO, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Molly Kuhs
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Emily Holcomb
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Cody Creech
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.,Center for Plant Science Innovation, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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6
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Teixeira PJPL, Colaianni NR, Law TF, Conway JM, Gilbert S, Li H, Salas-González I, Panda D, Del Risco NM, Finkel OM, Castrillo G, Mieczkowski P, Jones CD, Dangl JL. Specific modulation of the root immune system by a community of commensal bacteria. Proc Natl Acad Sci U S A 2021; 118:e2100678118. [PMID: 33879573 PMCID: PMC8072228 DOI: 10.1073/pnas.2100678118] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plants have an innate immune system to fight off potential invaders that is based on the perception of nonself or modified-self molecules. Microbe-associated molecular patterns (MAMPs) are evolutionarily conserved microbial molecules whose extracellular detection by specific cell surface receptors initiates an array of biochemical responses collectively known as MAMP-triggered immunity (MTI). Well-characterized MAMPs include chitin, peptidoglycan, and flg22, a 22-amino acid epitope found in the major building block of the bacterial flagellum, FliC. The importance of MAMP detection by the plant immune system is underscored by the large diversity of strategies used by pathogens to interfere with MTI and that failure to do so is often associated with loss of virulence. Yet, whether or how MTI functions beyond pathogenic interactions is not well understood. Here we demonstrate that a community of root commensal bacteria modulates a specific and evolutionarily conserved sector of the Arabidopsis immune system. We identify a set of robust, taxonomically diverse MTI suppressor strains that are efficient root colonizers and, notably, can enhance the colonization capacity of other tested commensal bacteria. We highlight the importance of extracellular strategies for MTI suppression by showing that the type 2, not the type 3, secretion system is required for the immunomodulatory activity of one robust MTI suppressor. Our findings reveal that root colonization by commensals is controlled by MTI, which, in turn, can be selectively modulated by specific members of a representative bacterial root microbiota.
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Affiliation(s)
- Paulo J P L Teixeira
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nicholas R Colaianni
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Theresa F Law
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jonathan M Conway
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Sarah Gilbert
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Haofan Li
- Department of Biology, Kenyon College, Gambier, OH 43022
| | - Isai Salas-González
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Darshana Panda
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nicole M Del Risco
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Omri M Finkel
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Gabriel Castrillo
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Piotr Mieczkowski
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jeffery L Dangl
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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7
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Salas-González I, Reyt G, Flis P, Custódio V, Gopaulchan D, Bakhoum N, Dew TP, Suresh K, Franke RB, Dangl JL, Salt DE, Castrillo G. Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis. Science 2021; 371:science.abd0695. [DOI: 10.1126/science.abd0695] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Isai Salas-González
- Curriculum in Bioinformatics and Computational Biology, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guilhem Reyt
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Paulina Flis
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Valéria Custódio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidad de Nova de Lisboa, Lisboa, Portugal
| | - David Gopaulchan
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Niokhor Bakhoum
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Tristan P. Dew
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Kiran Suresh
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Rochus Benni Franke
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Jeffery L. Dangl
- Curriculum in Bioinformatics and Computational Biology, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David E. Salt
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
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8
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Finkel OM, Salas-González I, Castrillo G, Conway JM, Law TF, Teixeira PJPL, Wilson ED, Fitzpatrick CR, Jones CD, Dangl JL. A single bacterial genus maintains root growth in a complex microbiome. Nature 2020. [PMID: 32999461 DOI: 10.1101/645655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Plants grow within a complex web of species that interact with each other and with the plant1-10. These interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development7-9,11-18. Here, to understand how interactions between microorganisms influence root growth in Arabidopsis, we established a model system for interactions between plants, microorganisms and the environment. We inoculated seedlings with a 185-member bacterial synthetic community, manipulated the abiotic environment and measured bacterial colonization of the plant. This enabled us to classify the synthetic community into four modules of co-occurring strains. We deconstructed the synthetic community on the basis of these modules, and identified interactions between microorganisms that determine root phenotype. These interactions primarily involve a single bacterial genus (Variovorax), which completely reverses the severe inhibition of root growth that is induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulates plant hormone levels to balance the effects of our ecologically realistic synthetic root community on root growth. We identify an auxin-degradation operon that is conserved in all available genomes of Variovorax and is necessary and sufficient for the reversion of root growth inhibition. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the stereotypic developmental programme of the root. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising ecological strategy for developing more resilient and productive crops.
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Affiliation(s)
- Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Theresa F Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paulo José Pereira Lima Teixeira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biology, 'Luiz de Queiroz' College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Ellie D Wilson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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9
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Reyt G, Chao Z, Flis P, Salas-González I, Castrillo G, Chao DY, Salt DE. Uclacyanin Proteins Are Required for Lignified Nanodomain Formation within Casparian Strips. Curr Biol 2020; 30:4103-4111.e6. [PMID: 32857976 PMCID: PMC7575197 DOI: 10.1016/j.cub.2020.07.095] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/14/2020] [Accepted: 07/28/2020] [Indexed: 01/09/2023]
Abstract
Casparian strips (CSs) are cell wall modifications of vascular plants restricting extracellular free diffusion into and out of the vascular system [1]. This barrier plays a critical role in controlling the acquisition of nutrients and water necessary for normal plant development [2-5]. CSs are formed by the precise deposition of a band of lignin approximately 2 μm wide and 150 nm thick spanning the apoplastic space between adjacent endodermal cells [6, 7]. Here, we identified a copper-containing protein, Uclacyanin1 (UCC1), that is sub-compartmentalized within the CS. UCC1 forms a central CS nanodomain in comparison with other CS-located proteins that are found to be mainly accumulated at the periphery of the CS. We found that loss-of-function of two uclacyanins (UCC1 and UCC2) reduces lignification specifically in this central CS nanodomain, revealing a nano-compartmentalized machinery for lignin polymerization. This loss of lignification leads to increased endodermal permeability and, consequently, to a loss of mineral nutrient homeostasis.
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Affiliation(s)
- Guilhem Reyt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Zhenfei Chao
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Paulina Flis
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Isai Salas-González
- Curriculum in Bioinformatics and Computational Biology, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriel Castrillo
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK.
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10
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Finkel OM, Salas-González I, Castrillo G, Conway JM, Law TF, Teixeira PJPL, Wilson ED, Fitzpatrick CR, Jones CD, Dangl JL. A single bacterial genus maintains root growth in a complex microbiome. Nature 2020; 587:103-108. [PMID: 32999461 DOI: 10.1038/s41586-020-2778-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/03/2020] [Indexed: 12/17/2022]
Abstract
Plants grow within a complex web of species that interact with each other and with the plant1-10. These interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development7-9,11-18. Here, to understand how interactions between microorganisms influence root growth in Arabidopsis, we established a model system for interactions between plants, microorganisms and the environment. We inoculated seedlings with a 185-member bacterial synthetic community, manipulated the abiotic environment and measured bacterial colonization of the plant. This enabled us to classify the synthetic community into four modules of co-occurring strains. We deconstructed the synthetic community on the basis of these modules, and identified interactions between microorganisms that determine root phenotype. These interactions primarily involve a single bacterial genus (Variovorax), which completely reverses the severe inhibition of root growth that is induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulates plant hormone levels to balance the effects of our ecologically realistic synthetic root community on root growth. We identify an auxin-degradation operon that is conserved in all available genomes of Variovorax and is necessary and sufficient for the reversion of root growth inhibition. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the stereotypic developmental programme of the root. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising ecological strategy for developing more resilient and productive crops.
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Affiliation(s)
- Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Theresa F Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paulo José Pereira Lima Teixeira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biology, 'Luiz de Queiroz' College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Ellie D Wilson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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11
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Ramirez-Villacis DX, Finkel OM, Salas-González I, Fitzpatrick CR, Dangl JL, Jones CD, Leon-Reyes A. Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate. mSphere 2020; 5:5/4/e00484-20. [PMID: 32817451 DOI: 10.46678/pb.20.1383160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis We found that a dose of 3.6 × 10-6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ∼14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by ∼17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains.IMPORTANCE Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.
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Affiliation(s)
- Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Galapagos Science Center, USFQ-UNC, San Cristobal, Galápagos, Ecuador
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12
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Ramirez-Villacis DX, Finkel OM, Salas-González I, Fitzpatrick CR, Dangl JL, Jones CD, Leon-Reyes A. Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate. mSphere 2020; 5:e00484-20. [PMID: 32817451 PMCID: PMC7426167 DOI: 10.1128/msphere.00484-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/23/2020] [Indexed: 01/22/2023] Open
Abstract
Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis We found that a dose of 3.6 × 10-6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ∼14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by ∼17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains.IMPORTANCE Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.
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Affiliation(s)
- Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Galapagos Science Center, USFQ-UNC, San Cristobal, Galápagos, Ecuador
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13
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Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, Teixeira PJPL, Dangl JL. The Plant Microbiome: From Ecology to Reductionism and Beyond. Annu Rev Microbiol 2020; 74:81-100. [PMID: 32530732 DOI: 10.1146/annurev-micro-022620-014327] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.
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Affiliation(s)
- Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Sarah Gilbert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Paulo José Pereira Lima Teixeira
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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14
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Finkel OM, Salas-González I, Castrillo G, Spaepen S, Law TF, Teixeira PJPL, Jones CD, Dangl JL. The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response. PLoS Biol 2019; 17:e3000534. [PMID: 31721759 PMCID: PMC6876890 DOI: 10.1371/journal.pbio.3000534] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/25/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Phosphate starvation response (PSR) in nonmycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms-the plant microbiota-are exposed to direct influence by the soil's phosphorus (P) content itself as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient and compared the composition of their shoot and root microbiota to wild-type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota than soil P concentrations in both roots and shoots. To dissect plant-microbe interactions under variable P conditions, we conducted a microbiota reconstitution experiment. Using a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift was accompanied by changes in microbiota composition: the genus Burkholderia was specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrated that in the absence of Burkholderia from the SynCom, plant shoots accumulated higher ortophosphate (Pi) levels than shoots colonized with the full SynCom but only under Pi starvation conditions. Therefore, Pi-stressed plants are susceptible to colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plant's Pi starvation.
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Affiliation(s)
- Omri M. Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stijn Spaepen
- Department Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Theresa F. Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paulo José Pereira Lima Teixeira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Corbin D. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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