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Pfeilmeier S, Werz A, Ote M, Bortfeld-Miller M, Kirner P, Keppler A, Hemmerle L, Gäbelein CG, Petti GC, Wolf S, Pestalozzi CM, Vorholt JA. Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens. Nat Microbiol 2024; 9:136-149. [PMID: 38172620 PMCID: PMC10769872 DOI: 10.1038/s41564-023-01555-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
In healthy plants, the innate immune system contributes to maintenance of microbiota homoeostasis, while disease can be associated with microbiome perturbation or dysbiosis, and enrichment of opportunistic plant pathogens like Xanthomonas. It is currently unclear whether the microbiota change occurs independently of the opportunistic pathogens or is caused by the latter. Here we tested if protein export through the type-2 secretion system (T2SS) by Xanthomonas causes microbiome dysbiosis in Arabidopsis thaliana in immunocompromised plants. We found that Xanthomonas strains secrete a cocktail of plant cell wall-degrading enzymes that promote Xanthomonas growth during infection. Disease severity and leaf tissue degradation were increased in A. thaliana mutants lacking the NADPH oxidase RBOHD. Experiments with gnotobiotic plants, synthetic bacterial communities and wild-type or T2SS-mutant Xanthomonas revealed that virulence and leaf microbiome composition are controlled by the T2SS. Overall, a compromised immune system in plants can enrich opportunistic pathogens, which damage leaf tissues and ultimately cause microbiome dysbiosis by facilitating growth of specific commensal bacteria.
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Affiliation(s)
- Sebastian Pfeilmeier
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
- Molecular Plant Pathology, Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
| | - Anja Werz
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Marine Ote
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Pascal Kirner
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Lucas Hemmerle
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | | | - Sarah Wolf
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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2
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Chavarro-Carrero EA, Snelders NC, Torres DE, Kraege A, López-Moral A, Petti GC, Punt W, Wieneke J, García-Velasco R, López-Herrera CJ, Seidl MF, Thomma BPHJ. The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization. PLoS Pathog 2024; 20:e1011866. [PMID: 38236788 PMCID: PMC10796067 DOI: 10.1371/journal.ppat.1011866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.
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Affiliation(s)
- Edgar A. Chavarro-Carrero
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Nick C. Snelders
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - David E. Torres
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Anton Kraege
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Ana López-Moral
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Gabriella C. Petti
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Wilko Punt
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Jan Wieneke
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Rómulo García-Velasco
- Laboratory of Phytopathology, Tenancingo University Center, Autonomous University of the State of Mexico, Tenancingo, State of Mexico, Mexico
| | - Carlos J. López-Herrera
- CSIC, Instituto de Agricultura Sostenible, Dept. Protección de Cultivos, C/Alameda del Obispo s/n, Córdoba, Spain
| | - Michael F. Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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Snelders NC, Boshoven JC, Song Y, Schmitz N, Fiorin GL, Rovenich H, van den Berg GCM, Torres DE, Petti GC, Prockl Z, Faino L, Seidl MF, Thomma BPHJ. A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria. New Phytol 2023; 237:944-958. [PMID: 36300791 DOI: 10.1111/nph.18576] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 08/22/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Plant pathogens secrete effector proteins to support host colonization through a wide range of molecular mechanisms, while plant immune systems evolved receptors to recognize effectors or their activities to mount immune responses to halt pathogens. Importantly, plants do not act as single organisms, but rather as holobionts that actively shape their microbiota as a determinant of health. The soil-borne fungal pathogen Verticillium dahliae was recently demonstrated to exploit the VdAve1 effector to manipulate the host microbiota to promote vascular wilt disease in the absence of the corresponding immune receptor Ve1. We identify a multiallelic V. dahliae gene displaying c. 65% sequence similarity to VdAve1, named VdAve1-like (VdAve1L), which shows extreme sequence variation, including alleles that encode dysfunctional proteins, indicative of selection pressure to overcome host recognition. We show that the orphan cell surface receptor Ve2, encoded at the Ve locus, does not recognize VdAve1L. Additionally, we demonstrate that the full-length variant VdAve1L2 possesses antimicrobial activity, like VdAve1, yet with a divergent activity spectrum, that is exploited by V. dahliae to mediate tomato colonization through the direct suppression of antagonistic Actinobacteria in the host microbiota. Our findings open up strategies for more targeted biocontrol against microbial plant pathogens.
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Affiliation(s)
- Nick C Snelders
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
- Theoretical Biology and Bioinformatics Group, Department of Biology, University of Utrecht, 3584CH, Utrecht, the Netherlands
| | - Jordi C Boshoven
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Yin Song
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Natalie Schmitz
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - David E Torres
- Theoretical Biology and Bioinformatics Group, Department of Biology, University of Utrecht, 3584CH, Utrecht, the Netherlands
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Gabriella C Petti
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Zoe Prockl
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
- Department of Ambiental Biology, Sapienza University of Rome, 00185, Rome, Italy
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics Group, Department of Biology, University of Utrecht, 3584CH, Utrecht, the Netherlands
| | - Bart P H J Thomma
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
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Snelders NC, Petti GC, van den Berg GCM, Seidl MF, Thomma BPHJ. An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation. Proc Natl Acad Sci U S A 2021; 118:e2110968118. [PMID: 34853168 PMCID: PMC8670511 DOI: 10.1073/pnas.2110968118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
Microbes typically secrete a plethora of molecules to promote niche colonization. Soil-dwelling microbes are well-known producers of antimicrobials that are exploited to outcompete microbial coinhabitants. Also, plant pathogenic microbes secrete a diversity of molecules into their environment for niche establishment. Upon plant colonization, microbial pathogens secrete so-called effector proteins that promote disease development. While such effectors are typically considered to exclusively act through direct host manipulation, we recently reported that the soil-borne, fungal, xylem-colonizing vascular wilt pathogen Verticillium dahliae exploits effector proteins with antibacterial properties to promote host colonization through the manipulation of beneficial host microbiota. Since fungal evolution preceded land plant evolution, we now speculate that a subset of the pathogen effectors involved in host microbiota manipulation evolved from ancient antimicrobial proteins of terrestrial fungal ancestors that served in microbial competition prior to the evolution of plant pathogenicity. Here, we show that V. dahliae has co-opted an ancient antimicrobial protein as effector, named VdAMP3, for mycobiome manipulation in planta. We show that VdAMP3 is specifically expressed to ward off fungal niche competitors during resting structure formation in senescing mesophyll tissues. Our findings indicate that effector-mediated microbiome manipulation by plant pathogenic microbes extends beyond bacteria and also concerns eukaryotic members of the plant microbiome. Finally, we demonstrate that fungal pathogens can exploit plant microbiome-manipulating effectors in a life stage-specific manner and that a subset of these effectors has evolved from ancient antimicrobial proteins of fungal ancestors that likely originally functioned in manipulation of terrestrial biota.
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Affiliation(s)
- Nick C Snelders
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne D-50674, Germany
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht 3584CH, The Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6708PB, The Netherlands
| | - Gabriella C Petti
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne D-50674, Germany
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6708PB, The Netherlands
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht 3584CH, The Netherlands
| | - Bart P H J Thomma
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne D-50674, Germany;
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6708PB, The Netherlands
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5
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Pfeilmeier S, Petti GC, Bortfeld-Miller M, Daniel B, Field CM, Sunagawa S, Vorholt JA. The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves. Nat Microbiol 2021; 6:852-864. [PMID: 34194036 PMCID: PMC7612668 DOI: 10.1038/s41564-021-00929-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
The plant microbiota consists of a multitude of microorganisms that can affect plant health and fitness. However, it is currently unclear how the plant shapes its leaf microbiota and what role the plant immune system plays in this process. Here, we evaluated Arabidopsis thaliana mutants with defects in different parts of the immune system for an altered bacterial community assembly using a gnotobiotic system. While higher-order mutants in receptors that recognize microbial features and in defence hormone signalling showed substantial microbial community alterations, the absence of the plant NADPH oxidase RBOHD caused the most pronounced change in the composition of the leaf microbiota. The rbohD knockout resulted in an enrichment of specific bacteria. Among these, we identified Xanthomonas strains as opportunistic pathogens that colonized wild-type plants asymptomatically but caused disease in rbohD knockout plants. Strain dropout experiments revealed that the lack of RBOHD unlocks the pathogenicity of individual microbiota members driving dysbiosis in rbohD knockout plants. For full protection, healthy plants require both a functional immune system and a microbial community. Our results show that the NADPH oxidase RBOHD is essential for microbiota homeostasis and emphasizes the importance of the plant immune system in controlling the leaf microbiota.
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Affiliation(s)
| | | | | | | | | | | | - Julia A. Vorholt
- Corresponding author: Correspondence should be addressed to J.A.V. ()
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6
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Snelders NC, Rovenich H, Petti GC, Rocafort M, van den Berg GCM, Vorholt JA, Mesters JR, Seidl MF, Nijland R, Thomma BPHJ. Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins. Nat Plants 2020; 6:1365-1374. [PMID: 33139860 DOI: 10.1038/s41477-020-00799-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 09/29/2020] [Indexed: 05/23/2023]
Abstract
During colonization of their hosts, pathogens secrete effector proteins to promote disease development through various mechanisms. Increasing evidence shows that the host microbiome plays a crucial role in health, and that hosts actively shape their microbiomes to suppress disease. We proposed that pathogens evolved to manipulate host microbiomes to their advantage in turn. Here, we show that the previously identified virulence effector VdAve1, secreted by the fungal plant pathogen Verticillium dahliae, displays antimicrobial activity and facilitates colonization of tomato and cotton through the manipulation of their microbiomes by suppressing antagonistic bacteria. Moreover, we show that VdAve1, and also the newly identified antimicrobial effector VdAMP2, are exploited for microbiome manipulation in the soil environment, where the fungus resides in absence of a host. In conclusion, we demonstrate that a fungal plant pathogen uses effector proteins to modulate microbiome compositions inside and outside the host, and propose that pathogen effector catalogues represent an untapped resource for new antibiotics.
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Affiliation(s)
- Nick C Snelders
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Hanna Rovenich
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Gabriella C Petti
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Mercedes Rocafort
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | | | - Jeroen R Mesters
- Institute of Biochemistry, University of Lübeck, Center for Structural and Cell Biology in Medicine, Lübeck, Germany
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Reindert Nijland
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Marine Animal Ecology Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands.
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Botanical Institute, Cologne, Germany.
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