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Metcalf CJE, Koskella B. Protective microbiomes can limit the evolution of host pathogen defense. Evol Lett 2019; 3:534-543. [PMID: 31636945 PMCID: PMC6791398 DOI: 10.1002/evl3.140] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/22/2019] [Accepted: 08/28/2019] [Indexed: 12/17/2022] Open
Abstract
The evolution of host immunity occurs in the context of the microbiome, but little theory exists to predict how resistance against pathogens might be influenced by the need to tolerate and regulate commensal microbiota. We present a general model to explore the optimal investment in host immunity under conditions in which the host can, versus cannot easily distinguish among commensal versus pathogenic bacteria, and when commensal microbiota can, versus cannot protect the host against the impacts of pathogen infection. We find that a loss of immune vigilance associated with innate immunity over evolutionary time can occur due to the challenge of discriminating between pathogenic and other microbe species. Further, we find the greater the protective effect of microbiome species, acting either directly or via competition with a pathogen, or the higher the costs of immunity, the more likely the loss of immune vigilance is. Conversely, this effect can be reversed when pathogens increase host mortality. Generally, the magnitude of costs of immunity required to allow evolution of decreased immune vigilance are predicted to be lowest when microbiome and pathogen species most resemble each other (in terms of host recognition), and when immune effects on the pathogen are weak. Our model framework makes explicit the core trade‐offs likely to shape the evolution of immunity in the context of microbiome/pathogen discrimination. We discuss how this informs interpretation of patterns and process in natural systems, including vulnerability to pathogen emergence.
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Affiliation(s)
- C Jessica E Metcalf
- Department of Ecology and Evolutionary Princeton University Princeton New Jersey 08540
| | - Britt Koskella
- Department of Integrative Biology University of California Berkeley Berkeley California 94720
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Zhang M, Xie S, Zhao Y, Meng X, Song L, Feng H, Huang L. Hce2 domain-containing effectors contribute to the full virulence of Valsa mali in a redundant manner. MOLECULAR PLANT PATHOLOGY 2019; 20:843-856. [PMID: 30912612 PMCID: PMC6637899 DOI: 10.1111/mpp.12796] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Valsa mali is the causal agent of apple Valsa canker, a destructive disease in East Asia. Effector proteins play important roles in the virulence of phytopathogenic fungi, and we identified five Hce2 domain-containing effectors (VmHEP1, VmHEP2, VmHEP3, VmHEP4 and VmHEP5) from the V. mali genome. Amongst these, VmHEP1 and VmHEP2 were found to be up-regulated during the early infection stage and VmHEP1 was also identified as a cell death inducer through its transient expression in Nicotiana benthamiana. Although the deletion of each single VmHEP gene did not lead to a reduction in virulence, the double-deletion of VmHEP1 and VmHEP2 notably attenuated V. mali virulence in both apple twigs and leaves. An evolutionary analysis revealed that VmHEP1 and VmHEP2 are two paralogues, under purifying selection. VmHEP1 and VmHEP2 are located next to each other on chromosome 11 as tandem genes with only a 604 bp physical distance. Interestingly, the deletion of VmHEP1 promoted the expression of VmHEP2 and, vice versa, the deletion of VmHEP2 promoted the expression of VmHEP1. The present results provide insights into the functions of Hce2 domain-containing effectors acting as virulence factors of V. mali, and provide a new perspective regarding the contribution of tandem genes to the virulence of phytopathogenic fungi.
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Affiliation(s)
- Mian Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Shichang Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Yuhuan Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Xiang Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Linlin Song
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Hao Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
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Mohd-Assaad N, McDonald BA, Croll D. The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses. Environ Microbiol 2019; 21:2677-2695. [PMID: 30838748 DOI: 10.1111/1462-2920.14583] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/23/2019] [Accepted: 03/04/2019] [Indexed: 01/28/2023]
Abstract
Plant pathogens secrete effector proteins to manipulate the host and facilitate infection. Cognate hosts trigger strong defence responses upon detection of these effectors. Consequently, pathogens and hosts undergo rapid coevolutionary arms races driven by adaptive evolution of effectors and receptors. Because of their high rate of turnover, most effectors are thought to be species-specific and the evolutionary trajectories are poorly understood. Here, we investigate the necrosis-inducing protein 1 (NIP1) effector in the multihost pathogen genus Rhynchosporium. We retraced the evolutionary history of the NIP1 locus using whole-genome assemblies of 146 strains covering four closely related species. NIP1 orthologues were present in all species but the locus consistently segregated presence-absence polymorphisms suggesting long-term balancing selection. We also identified previously unknown paralogues of NIP1 that were shared among multiple species and showed substantial copy-number variation within R. commune. The NIP1A paralogue was under significant positive selection suggesting that NIP1A is the dominant effector variant coevolving with host immune receptors. Consistent with this prediction, we found that copy number variation at NIP1A had a stronger effect on virulence than NIP1B. Our analyses unravelled the origins and diversification mechanisms of a pathogen effector family shedding light on how pathogens gain adaptive genetic variation.
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Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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Malinich EA, Wang K, Mukherjee PK, Kolomiets M, Kenerley CM. Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots. BMC Genomics 2019; 20:280. [PMID: 30971198 PMCID: PMC6458689 DOI: 10.1186/s12864-019-5651-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 03/27/2019] [Indexed: 12/16/2022] Open
Abstract
Background Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-industrial products. To better take advantage of this fungal-plant symbiosis it is necessary to obtain detailed knowledge of which genes Trichoderma utilizes during interaction with its plant host. In this study, we explored the transcriptional activity undergone by T. virens during two phases of symbiosis with maize; recognition of roots and after ingress into the root cortex. Results We present a model of T. virens – maize interaction wherein T. virens experiences global repression of transcription upon recognition of maize roots and then induces expression of a broad spectrum of genes during colonization of maize roots. The genes expressed indicate that, during colonization of maize roots, T. virens modulates biosynthesis of phytohormone-like compounds, secretes a plant-environment specific array of cell wall degrading enzymes and secondary metabolites, remodels both actin-based and cell membrane structures, and shifts metabolic activity. We also highlight transcription factors and signal transduction genes important in future research seeking to unravel the molecular mechanisms of T. virens activity in maize roots. Conclusions T. virens displays distinctly different transcriptional profiles between recognizing the presence of maize roots and active colonization of these roots. A though understanding of these processes will allow development of T. virens as a bio-control agent. Further, the publication of these datasets will target future research endeavors specifically to genes of interest when considering T. virens – maize symbiosis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5651-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth A Malinich
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Ken Wang
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Prasun K Mukherjee
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Michael Kolomiets
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Charles M Kenerley
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
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Panstruga R, Kuhn H. Mutual interplay between phytopathogenic powdery mildew fungi and other microorganisms. MOLECULAR PLANT PATHOLOGY 2019; 20:463-470. [PMID: 30467940 PMCID: PMC6637862 DOI: 10.1111/mpp.12771] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Powdery mildew is a common and widespread plant disease of considerable agronomic relevance. It is caused by obligate biotrophic fungal pathogens which, in most cases, epiphytically colonize aboveground plant tissues. The disease has been typically studied as a binary interaction of the fungal pathogen with its plant hosts, neglecting, for the most part, the mutual interplay with the wealth of other microorganisms residing in the phyllo- and/or rhizosphere and roots. However, the establishment of powdery mildew disease can be impacted by the presence/absence of host-associated microbiota (epi- and endophytes) and, conversely, plant colonization by powdery mildew fungi might disturb indigenous microbial community structures. In addition, other (foliar) phytopathogens could interact with powdery mildews, and mycoparasites may affect the outcome of plant-powdery mildew interactions. In this review, we discuss the current knowledge regarding the intricate and multifaceted interplay of powdery mildew fungi, host plants and other microorganisms, and outline current gaps in our knowledge, thereby setting the basis for potential future research directions.
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Affiliation(s)
- Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityWorringerweg 1Aachen52056Germany
| | - Hannah Kuhn
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityWorringerweg 1Aachen52056Germany
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Haueisen J, Möller M, Eschenbrenner CJ, Grandaubert J, Seybold H, Adamiak H, Stukenbrock EH. Highly flexible infection programs in a specialized wheat pathogen. Ecol Evol 2019; 9:275-294. [PMID: 30680113 PMCID: PMC6342133 DOI: 10.1002/ece3.4724] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/21/2022] Open
Abstract
Many filamentous plant pathogens exhibit high levels of genomic variability, yet the impact of this variation on host-pathogen interactions is largely unknown. We have addressed host specialization in the wheat pathogen Zymoseptoria tritici. Our study builds on comparative analyses of infection and gene expression phenotypes of three isolates and reveals the extent to which genomic variation translates into phenotypic variation. The isolates exhibit genetic and genomic variation but are similarly virulent. By combining confocal microscopy, disease monitoring, staining of ROS, and comparative transcriptome analyses, we conducted a detailed comparison of the infection processes of these isolates in a susceptible wheat cultivar. We characterized four core infection stages: establishment, biotrophic growth, lifestyle transition, and necrotrophic growth and asexual reproduction that are shared by the three isolates. However, we demonstrate differentiated temporal and spatial infection development and significant differences in the expression profiles of the three isolates during the infection stages. More than 20% of the genes were differentially expressed and these genes were located significantly closer to transposable elements, suggesting an impact of epigenetic regulation. Further, differentially expressed genes were enriched in effector candidates suggesting that isolate-specific strategies for manipulating host defenses are present in Z. tritici. We demonstrate that individuals of a host-specialized pathogen have highly differentiated infection programs characterized by flexible infection development and functional redundancy. This illustrates how high genetic diversity in pathogen populations results in highly differentiated infection phenotypes, which fact needs to be acknowledged to understand host-pathogen interactions and pathogen evolution.
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Affiliation(s)
- Janine Haueisen
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
| | - Mareike Möller
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
| | - Christoph J. Eschenbrenner
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
| | - Jonathan Grandaubert
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Fungal Biology and PathogenicityInstitute PasteurParisFrance
| | - Heike Seybold
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
| | - Holger Adamiak
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
| | - Eva H. Stukenbrock
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
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Pascale A, Proietti S, Pantelides IS, Stringlis IA. Modulation of the Root Microbiome by Plant Molecules: The Basis for Targeted Disease Suppression and Plant Growth Promotion. FRONTIERS IN PLANT SCIENCE 2019; 10:1741. [PMID: 32038698 PMCID: PMC6992662 DOI: 10.3389/fpls.2019.01741] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/11/2019] [Indexed: 05/18/2023]
Abstract
Plants host a mesmerizing diversity of microbes inside and around their roots, known as the microbiome. The microbiome is composed mostly of fungi, bacteria, oomycetes, and archaea that can be either pathogenic or beneficial for plant health and fitness. To grow healthy, plants need to surveil soil niches around the roots for the detection of pathogenic microbes, and in parallel maximize the services of beneficial microbes in nutrients uptake and growth promotion. Plants employ a palette of mechanisms to modulate their microbiome including structural modifications, the exudation of secondary metabolites and the coordinated action of different defence responses. Here, we review the current understanding on the composition and activity of the root microbiome and how different plant molecules can shape the structure of the root-associated microbial communities. Examples are given on interactions that occur in the rhizosphere between plants and soilborne fungi. We also present some well-established examples of microbiome harnessing to highlight how plants can maximize their fitness by selecting their microbiome. Understanding how plants manipulate their microbiome can aid in the design of next-generation microbial inoculants for targeted disease suppression and enhanced plant growth.
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Affiliation(s)
- Alberto Pascale
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Silvia Proietti
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Iakovos S. Pantelides
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
- *Correspondence: Iakovos S. Pantelides, ; Ioannis A. Stringlis,
| | - Ioannis A. Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
- *Correspondence: Iakovos S. Pantelides, ; Ioannis A. Stringlis,
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Zembek P, Danilecka A, Hoser R, Eschen-Lippold L, Benicka M, Grech-Baran M, Rymaszewski W, Barymow-Filoniuk I, Morgiewicz K, Kwiatkowski J, Piechocki M, Poznanski J, Lee J, Hennig J, Krzymowska M. Two Strategies of Pseudomonas syringae to Avoid Recognition of the HopQ1 Effector in Nicotiana Species. FRONTIERS IN PLANT SCIENCE 2018; 9:978. [PMID: 30042777 PMCID: PMC6048448 DOI: 10.3389/fpls.2018.00978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/15/2018] [Indexed: 05/18/2023]
Abstract
Pseudomonas syringae employs a battery of type three secretion effectors to subvert plant immune responses. In turn, plants have developed receptors that recognize some of the bacterial effectors. Two strain-specific HopQ1 effector variants (for Hrp outer protein Q) from the pathovars phaseolicola 1448A (Pph) and tomato DC3000 (Pto) showed considerable differences in their ability to evoke disease symptoms in Nicotiana benthamiana. Surprisingly, the variants differ by only six amino acids located mostly in the N-terminal disordered region of HopQ1. We found that the presence of serine 87 and leucine 91 renders PtoHopQ1 susceptible to N-terminal processing by plant proteases. Substitutions at these two positions did not strongly affect PtoHopQ1 virulence properties in a susceptible host but they reduced bacterial growth and accelerated onset of cell death in a resistant host, suggesting that N-terminal mutations rendered PtoHopQ1 susceptible to processing in planta and, thus, represent a mechanism of recognition avoidance. Furthermore, we found that co-expression of HopR1, another effector encoded within the same gene cluster masks HopQ1 recognition in a strain-dependent manner. Together, these data suggest that HopQ1 is under high host-pathogen co-evolutionary selection pressure and P. syringae may have evolved differential effector processing or masking as two independent strategies to evade HopQ1 recognition, thus revealing another level of complexity in plant - microbe interactions.
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Affiliation(s)
- Patrycja Zembek
- Institute of Biochemistry and Biophysics (PAS), Warsaw, Poland
| | | | - Rafał Hoser
- Institute of Biochemistry and Biophysics (PAS), Warsaw, Poland
| | | | - Marta Benicka
- Institute of Biochemistry and Biophysics (PAS), Warsaw, Poland
| | | | | | | | | | | | | | | | - Justin Lee
- Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Jacek Hennig
- Institute of Biochemistry and Biophysics (PAS), Warsaw, Poland
| | - Magdalena Krzymowska
- Institute of Biochemistry and Biophysics (PAS), Warsaw, Poland
- *Correspondence: Magdalena Krzymowska,
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