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Abstract
The rhizosphere microbiome of plants is essential for plant growth and health. Recent studies have shown that upon infection of leaves with a foliar pathogen, the composition of the root microbiome is altered and enriched with bacteria that in turn can systemically protect the plant against the foliar pathogen. This protective effect is extended to successive populations of plants that are grown on soil that was first conditioned by pathogen-infected plants, a phenomenon that was coined "the soil-borne legacy." Here we provide a detailed protocol for soil-borne legacy experiments with the model plant Arabidopsis thaliana after infection with the obligate biotrophic pathogen Hyaloperonospora arabidopsidis. This protocol can easily be extended to infection with other pathogens or even infestation with herbivorous insects and can function as a blueprint for soil-borne legacy experiments with crop species.
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Affiliation(s)
- Gilles Vismans
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Jelle Spooren
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands.
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2
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Bakker PAHM, Berendsen RL, Van Pelt JA, Vismans G, Yu K, Li E, Van Bentum S, Poppeliers SWM, Sanchez Gil JJ, Zhang H, Goossens P, Stringlis IA, Song Y, de Jonge R, Pieterse CMJ. The Soil-Borne Identity and Microbiome-Assisted Agriculture: Looking Back to the Future. Mol Plant 2020; 13:1394-1401. [PMID: 32979564 DOI: 10.1016/j.molp.2020.09.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Looking forward includes looking back every now and then. In 2007, David Weller looked back at 30 years of biocontrol of soil-borne pathogens by Pseudomonas and signified that the progress made over decades of research has provided a firm foundation to formulate current and future research questions. It has been recognized for more than a century that soil-borne microbes play a significant role in plant growth and health. The recent application of high-throughput omics technologies has enabled detailed dissection of the microbial players and molecular mechanisms involved in the complex interactions in plant-associated microbiomes. Here, we highlight old and emerging plant microbiome concepts related to plant disease control, and address perspectives that modern and emerging microbiomics technologies can bring to functionally characterize and exploit plant-associated microbiomes for the benefit of plant health in future microbiome-assisted agriculture.
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Affiliation(s)
- Peter A H M Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Johan A Van Pelt
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Gilles Vismans
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ke Yu
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Erqin Li
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Sietske Van Bentum
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Sanne W M Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Juan J Sanchez Gil
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Hao Zhang
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Pim Goossens
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Yang Song
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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3
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van der Horst S, van Butselaar T, Zhang H, Vismans G, Steenbergen M, Courbier S, Neilen M, Küpers JJ. Bringing together Europe's young plant scientists. New Phytol 2019; 222:29-32. [PMID: 30815945 DOI: 10.1111/nph.15691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Sjors van der Horst
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Tijmen van Butselaar
- Plant-Microbe Interactions, Utrecht University, Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Hao Zhang
- Plant-Microbe Interactions, Utrecht University, Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Gilles Vismans
- Plant-Microbe Interactions, Utrecht University, Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Merel Steenbergen
- Plant-Microbe Interactions, Utrecht University, Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Sarah Courbier
- Plant-Microbe Interactions, Utrecht University, Padualaan 8, 3584CH Utrecht, the Netherlands
- Plant Ecophysiology, Utrecht University, Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Manon Neilen
- Plant-Microbe Interactions, Utrecht University, Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Jesse J Küpers
- Plant Ecophysiology, Utrecht University, Padualaan 8, 3584CH Utrecht, the Netherlands
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Berendsen RL, Vismans G, Yu K, Song Y, de Jonge R, Burgman WP, Burmølle M, Herschend J, Bakker PAHM, Pieterse CMJ. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J 2018. [PMID: 29520025 PMCID: PMC5956071 DOI: 10.1038/s41396-018-0093-1] [Citation(s) in RCA: 361] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Disease suppressive soils typically develop after a disease outbreak due to the subsequent assembly of protective microbiota in the rhizosphere. The role of the plant immune system in the assemblage of a protective rhizosphere microbiome is largely unknown. In this study, we demonstrate that Arabidopsis thaliana specifically promotes three bacterial species in the rhizosphere upon foliar defense activation by the downy mildew pathogen Hyaloperonospora arabidopsidis. The promoted bacteria were isolated and found to interact synergistically in biofilm formation in vitro. Although separately these bacteria did not affect the plant significantly, together they induced systemic resistance against downy mildew and promoted growth of the plant. Moreover, we show that the soil-mediated legacy of a primary population of downy mildew infected plants confers enhanced protection against this pathogen in a second population of plants growing in the same soil. Together our results indicate that plants can adjust their root microbiome upon pathogen infection and specifically recruit a group of disease resistance-inducing and growth-promoting beneficial microbes, therewith potentially maximizing the chance of survival of their offspring that will grow in the same soil.
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Affiliation(s)
- Roeland L Berendsen
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Gilles Vismans
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ke Yu
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Yang Song
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Jiangsu Provincial Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
| | - Wilco P Burgman
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, København, Denmark
| | - Jakob Herschend
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, København, Denmark
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Vismans G, van der Meer T, Langevoort O, Schreuder M, Bouwmeester H, Peisker H, Dörman P, Ketelaar T, van der Krol A. Low-Phosphate Induction of Plastidal Stromules Is Dependent on Strigolactones But Not on the Canonical Strigolactone Signaling Component MAX2. Plant Physiol 2016; 172:2235-2244. [PMID: 27760882 PMCID: PMC5129712 DOI: 10.1104/pp.16.01146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/13/2016] [Indexed: 05/18/2023]
Abstract
Stromules are highly dynamic protrusions of the plastids in plants. Several factors, such as drought and light conditions, influence the stromule frequency (SF) in a positive or negative way. A relatively recently discovered class of plant hormones are the strigolactones; strigolactones inhibit branching of the shoots and promote beneficial interactions between roots and arbuscular mycorrhizal fungi. Here, we investigate the link between the formation of stromules and strigolactones. This research shows a strong link between strigolactones and the formation of stromules: SF correlates with strigolactone levels in the wild type and strigolactone mutants (max2-1 max3-9), and SF is stimulated by strigolactone GR24 and reduced by strigolactone inhibitor D2.
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Affiliation(s)
- Gilles Vismans
- Laboratory of Plant Physiology (G.V., T.v.d.M., O.L., M.S., A.v.d.K.) and Laboratory of Cell Biology (G.V., T.v.d.M., O.L., T.K), Wageningen University, 6708 PB Wageningen, The Netherlands; and
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53113 Bonn, Germany (H.P., P.D.)
| | - Tom van der Meer
- Laboratory of Plant Physiology (G.V., T.v.d.M., O.L., M.S., A.v.d.K.) and Laboratory of Cell Biology (G.V., T.v.d.M., O.L., T.K), Wageningen University, 6708 PB Wageningen, The Netherlands; and
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53113 Bonn, Germany (H.P., P.D.)
| | - Olivier Langevoort
- Laboratory of Plant Physiology (G.V., T.v.d.M., O.L., M.S., A.v.d.K.) and Laboratory of Cell Biology (G.V., T.v.d.M., O.L., T.K), Wageningen University, 6708 PB Wageningen, The Netherlands; and
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53113 Bonn, Germany (H.P., P.D.)
| | - Marielle Schreuder
- Laboratory of Plant Physiology (G.V., T.v.d.M., O.L., M.S., A.v.d.K.) and Laboratory of Cell Biology (G.V., T.v.d.M., O.L., T.K), Wageningen University, 6708 PB Wageningen, The Netherlands; and
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53113 Bonn, Germany (H.P., P.D.)
| | - Harro Bouwmeester
- Laboratory of Plant Physiology (G.V., T.v.d.M., O.L., M.S., A.v.d.K.) and Laboratory of Cell Biology (G.V., T.v.d.M., O.L., T.K), Wageningen University, 6708 PB Wageningen, The Netherlands; and
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53113 Bonn, Germany (H.P., P.D.)
| | - Helga Peisker
- Laboratory of Plant Physiology (G.V., T.v.d.M., O.L., M.S., A.v.d.K.) and Laboratory of Cell Biology (G.V., T.v.d.M., O.L., T.K), Wageningen University, 6708 PB Wageningen, The Netherlands; and
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53113 Bonn, Germany (H.P., P.D.)
| | - Peter Dörman
- Laboratory of Plant Physiology (G.V., T.v.d.M., O.L., M.S., A.v.d.K.) and Laboratory of Cell Biology (G.V., T.v.d.M., O.L., T.K), Wageningen University, 6708 PB Wageningen, The Netherlands; and
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53113 Bonn, Germany (H.P., P.D.)
| | - Tijs Ketelaar
- Laboratory of Plant Physiology (G.V., T.v.d.M., O.L., M.S., A.v.d.K.) and Laboratory of Cell Biology (G.V., T.v.d.M., O.L., T.K), Wageningen University, 6708 PB Wageningen, The Netherlands; and
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53113 Bonn, Germany (H.P., P.D.)
| | - Alexander van der Krol
- Laboratory of Plant Physiology (G.V., T.v.d.M., O.L., M.S., A.v.d.K.) and Laboratory of Cell Biology (G.V., T.v.d.M., O.L., T.K), Wageningen University, 6708 PB Wageningen, The Netherlands; and
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53113 Bonn, Germany (H.P., P.D.)
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Madsen CK, Vismans G, Brinch-Pedersen H. The PARS sequence increase the efficiency of stable Pichia pastoris transformation. J Microbiol Methods 2016; 129:1-7. [PMID: 27444547 DOI: 10.1016/j.mimet.2016.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/12/2016] [Accepted: 07/16/2016] [Indexed: 10/21/2022]
Abstract
The methylotrophic yeast Pichia pastoris is a popular host for recombinant expression of proteins. Plasmids containing the Pichia autonomously replicating sequence (PARS) transform P. pastoris with higher efficiency than linear DNA equipped with termini designed for homologous recombination. Moreover, PARS containing constructs provide higher protein yields. Unfortunately, these autonomous plasmids are inherently unstable and the preferred method of P. pastoris transformation is therefore stable integration in the genome by homologous recombination. In the present study we report that a novel combination of PARS and linearization of plasmids for P. pastoris transformation serves to significantly increase the transformation efficiency. Moreover, it is demonstrated that the constructs do not re-circularize but integrate stably into the P. pastoris genome.
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Affiliation(s)
- Claus Krogh Madsen
- Department of Molecular Biology and Genetics, Section for Crop Genetics and Biotechnology, Aarhus University, Forsogsvej 1, 4200 Slagelse, Denmark.
| | - Gilles Vismans
- Wageningen University, 6708PB Wageningen, The Netherlands
| | - Henrik Brinch-Pedersen
- Department of Molecular Biology and Genetics, Section for Crop Genetics and Biotechnology, Aarhus University, Forsogsvej 1, 4200 Slagelse, Denmark
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