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Martel A, Ruiz-Bedoya T, Breit-McNally C, Laflamme B, Desveaux D, Guttman DS. The ETS-ETI cycle: evolutionary processes and metapopulation dynamics driving the diversification of pathogen effectors and host immune factors. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102011. [PMID: 33677388 DOI: 10.1016/j.pbi.2021.102011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 05/13/2023]
Abstract
The natural diversity of pathogen effectors and host immune components represents a snapshot of the underlying evolutionary processes driving the host-pathogen arms race. In plants, this arms race is manifested by an ongoing cycle of disease and resistance driven by pathogenic effectors that promote disease (effector-triggered susceptibility; ETS) and plant resistance proteins that recognize effector activity to trigger immunity (effector-triggered immunity; ETI). Here we discuss how this ongoing ETS-ETI cycle has shaped the natural diversity of both plant resistance proteins and pathogen effectors. We focus on the evolutionary forces that drive the diversification of the molecules that determine the outcome of plant-pathogen interactions and introduce the concept of metapopulation dynamics (i.e., the introduction of genetic variation from conspecific organisms in different populations) as an alternative mechanism that can introduce and maintain diversity in both host and pathogen populations.
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Affiliation(s)
- Alexandre Martel
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Tatiana Ruiz-Bedoya
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Clare Breit-McNally
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Bradley Laflamme
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
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Gopalan-Nair R, Jardinaud MF, Legrand L, Landry D, Barlet X, Lopez-Roques C, Vandecasteele C, Bouchez O, Genin S, Guidot A. Convergent Rewiring of the Virulence Regulatory Network Promotes Adaptation of Ralstonia solanacearum on Resistant Tomato. Mol Biol Evol 2021; 38:1792-1808. [PMID: 33306125 PMCID: PMC8097285 DOI: 10.1093/molbev/msaa320] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The evolutionary and adaptive potential of a pathogen is a key determinant for successful host colonization and proliferation but remains poorly known for most of the pathogens. Here, we used experimental evolution combined with phenotyping, genomics, and transcriptomics to estimate the adaptive potential of the bacterial plant pathogen Ralstonia solanacearum to overcome the quantitative resistance of the tomato cultivar Hawaii 7996. After serial passaging over 300 generations, we observed pathogen adaptation to within-plant environment of the resistant cultivar but no plant resistance breakdown. Genomic sequence analysis of the adapted clones revealed few genetic alterations, but we provide evidence that all but one were gain of function mutations. Transcriptomic analyses revealed that even if different adaptive events occurred in independently evolved clones, there is convergence toward a global rewiring of the virulence regulatory network as evidenced by largely overlapping gene expression profiles. A subset of four transcription regulators, including HrpB, the activator of the type 3 secretion system regulon and EfpR, a global regulator of virulence and metabolic functions, emerged as key nodes of this regulatory network that are frequently targeted to redirect the pathogen’s physiology and improve its fitness in adverse conditions. Significant transcriptomic variations were also detected in evolved clones showing no genomic polymorphism, suggesting that epigenetic modifications regulate expression of some of the virulence network components and play a major role in adaptation as well.
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Affiliation(s)
| | | | - Ludovic Legrand
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - David Landry
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Xavier Barlet
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | | | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRAE, US 1426, Castanet-Tolosan, France
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Alice Guidot
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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Manriquez B, Muller D, Prigent-Combaret C. Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities. Front Microbiol 2021; 12:619122. [PMID: 34025595 PMCID: PMC8137971 DOI: 10.3389/fmicb.2021.619122] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
In natural environments, microbial communities must constantly adapt to stressful environmental conditions. The genetic and phenotypic mechanisms underlying the adaptive response of microbial communities to new (and often complex) environments can be tackled with a combination of experimental evolution and next generation sequencing. This combination allows to analyse the real-time evolution of microbial populations in response to imposed environmental factors or during the interaction with a host, by screening for phenotypic and genotypic changes over a multitude of identical experimental cycles. Experimental evolution (EE) coupled with comparative genomics has indeed facilitated the monitoring of bacterial genetic evolution and the understanding of adaptive evolution processes. Basically, EE studies had long been done on single strains, allowing to reveal the dynamics and genetic targets of natural selection and to uncover the correlation between genetic and phenotypic adaptive changes. However, species are always evolving in relation with other species and have to adapt not only to the environment itself but also to the biotic environment dynamically shaped by the other species. Nowadays, there is a growing interest to apply EE on microbial communities evolving under natural environments. In this paper, we provide a non-exhaustive review of microbial EE studies done with systems of increasing complexity (from single species, to synthetic communities and natural communities) and with a particular focus on studies between plants and plant-associated microorganisms. We highlight some of the mechanisms controlling the functioning of microbial species and their adaptive responses to environment changes and emphasize the importance of considering bacterial communities and complex environments in EE studies.
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Affiliation(s)
| | | | - Claire Prigent-Combaret
- UMR 5557 Ecologie Microbienne, VetAgro Sup, CNRS, INRAE, University of Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
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Lievens EJP, Michalakis Y, Lenormand T. Trait‐specific trade‐offs prevent niche expansion in two parasites. J Evol Biol 2020; 33:1704-1714. [DOI: 10.1111/jeb.13708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Eva J. P. Lievens
- CEFE, CNRS Univ MontpellierUniv Paul Valéry Montpellier 3EPHEIRD Montpellier France
- UMR 5290 MIVEGEC Univ MontpellierCNRSIRD Montpellier Cedex 5 France
| | - Yannis Michalakis
- UMR 5290 MIVEGEC Univ MontpellierCNRSIRD Montpellier Cedex 5 France
- Centre of Research in Ecology and Evolution of Diseases (CREES) Montpellier France
| | - Thomas Lenormand
- CEFE, CNRS Univ MontpellierUniv Paul Valéry Montpellier 3EPHEIRD Montpellier France
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Burghardt LT. Evolving together, evolving apart: measuring the fitness of rhizobial bacteria in and out of symbiosis with leguminous plants. THE NEW PHYTOLOGIST 2020; 228:28-34. [PMID: 31276218 DOI: 10.1111/nph.16045] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/20/2019] [Indexed: 05/11/2023]
Abstract
Most plant-microbe interactions are facultative, with microbes experiencing temporally and spatially variable selection. How this variation affects microbial evolution is poorly understood. Given its tractability and ecological and agricultural importance, the legume-rhizobia nitrogen-fixing symbiosis is a powerful model for identifying traits and genes underlying bacterial fitness. New technologies allow high-throughput measurement of the relative fitness of bacterial mutants, strains and species in mixed inocula in the host, rhizosphere and soil environments. I consider how host genetic variation (G × G), other environmental factors (G × E), and host life-cycle variation may contribute to the maintenance of genetic variation and adaptive trajectories of rhizobia - and, potentially, other facultative symbionts. Lastly, I place these findings in the context of developing beneficial inoculants in a changing climate.
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Affiliation(s)
- Liana T Burghardt
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St Paul, MN, 55108, USA
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Hernandez CA, Koskella B. Phage resistance evolution in vitro is not reflective of in vivo outcome in a plant-bacteria-phage system. Evolution 2019; 73:2461-2475. [PMID: 31433508 DOI: 10.1111/evo.13833] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022]
Abstract
The evolution of resistance to parasites is fundamentally important to disease ecology, yet we remain unable to predict when and how resistance will evolve. This is largely due to the context-dependent nature of host-parasite interactions, as the benefit of resistance will depend on the abiotic and biotic environment. Through experimental evolution of the plant pathogenic bacterium Pseudomonas syringae and two lytic bacteriophages across two different environments (high-nutrient media and the tomato leaf apoplast), we demonstrate that de novo evolution of resistance is negligible in planta despite high levels of resistance evolution in vitro. We find no evidence supporting the evolution of phage-selected resistance in planta despite multiple passaging experiments, multiple assays for resistance, and high multiplicities of infection. Additionally, we find that phage-resistant mutants (evolved in vitro) did not realize a fitness benefit over phage-sensitive cells when grown in planta in the presence of phage, despite reduced growth of sensitive cells, evidence of phage replication in planta, and a large fitness benefit in the presence of phage observed in vitro. Thus, this context-dependent benefit of phage resistance led to different evolutionary outcomes across environments. These results underscore the importance of studying the evolution of parasite resistance in ecologically relevant environments.
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Affiliation(s)
- Catherine A Hernandez
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
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Burghardt LT, Epstein B, Tiffin P. Legacy of prior host and soil selection on rhizobial fitness in planta. Evolution 2019; 73:2013-2023. [PMID: 31334838 DOI: 10.1111/evo.13807] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/03/2023]
Abstract
Measuring selection acting on microbial populations in natural or even seminatural environments is challenging because many microbial populations experience variable selection. The majority of rhizobial bacteria are found in the soil. However, they also live symbiotically inside nodules of legume hosts and each nodule can release thousands of daughter cells back into the soil. We tested how past selection (i.e., legacies) by two plant genotypes and by the soil alone affected selection and genetic diversity within a population of 101 strains of Ensifer meliloti. We also identified allelic variants most strongly associated with soil- and host-dependent fitness. In addition to imposing direct selection on rhizobia populations, soil and host environments had lasting effects across host generations. Host presence and genotype during the legacy period explained 22% and 12% of the variance in the strain composition of nodule communities in the second cohort, respectively. Although strains with high host fitness in the legacy cohort tended to be enriched in the second cohort, the diversity of the strain community was greater when the second cohort was preceded by host rather than soil legacies. Our results indicate the potential importance of soil selection driving the evolution of these plant-associated microbes.
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Affiliation(s)
- Liana T Burghardt
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
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Wu H, Chen H, Jin C, Tang C, Zhang Y. The chirality of imazethapyr herbicide selectively affects the bacterial community in soybean field soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:2531-2546. [PMID: 30474807 DOI: 10.1007/s11356-018-3736-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
The chiral herbicide imazethapyr (IM) is frequently used to control weeds in soybean fields in northeast China. However, the impact of IM enantiomers on microbial communities in soil is still unknown. Genetic markers (16S rRNA V3-V4 regions) were used to characterize and evaluate the variation of the bacterial communities potentially effected by IM enantiomers. Globally, the bacterial community structure based on the OTU profiles in (-)-R-IM-treated soils was significantly different from those in (+)-S-IM-treated soils, and the differences were enlarged with the treatment dose increasing. Interestingly, the Rhizobiaceae family and several other beneficial bacteria, including Bradyrhizobium, Methylobacterium, and Paenibacillus, were strongly enriched in (-)-R-IM treatment compared to (+)-S-IM treatment. In contrast, the pathogenic bacteria, including Erwinia, Pseudomonas, Burkholderia, Streptomyces, and Agrobacterium, were suppressed in the presence of (-)-R-IM compared to (+)-S-IM. Furthermore, we also observed that the bacterial community structure in (-)-R-IM-treated soils was more quickly restored to its original state compared with those in (+)-S-IM-treated soils. These findings unveil a new role of chiral herbicide in the development of soil microbial ecology and provide theoretical support for the application of low-persistence, high-efficiency, and eco-friendly optical rotatory (-)-R-IM.
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Affiliation(s)
- Hao Wu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Hongshan Chen
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Chongwei Jin
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Caixian Tang
- Department of Agricultural Sciences, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Yongsong Zhang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, China.
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Giraud T, Koskella B, Laine AL. Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution. Mol Ecol 2018; 26:1703-1710. [PMID: 28409900 DOI: 10.1111/mec.14091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 02/14/2017] [Accepted: 03/02/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
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Agha R, Gross A, Rohrlack T, Wolinska J. Adaptation of a Chytrid Parasite to Its Cyanobacterial Host Is Hampered by Host Intraspecific Diversity. Front Microbiol 2018; 9:921. [PMID: 29867832 PMCID: PMC5952108 DOI: 10.3389/fmicb.2018.00921] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/20/2018] [Indexed: 01/08/2023] Open
Abstract
Experimental evolution can be used to test for and characterize parasite and pathogen adaptation. We undertook a serial-passage experiment in which a single parasite population of the obligate fungal (chytrid) parasite Rhizophydium megarrhizum was maintained over a period of 200 days under different mono- and multiclonal compositions of its phytoplankton host, the bloom-forming cyanobacterium Planktothrix. Despite initially inferior performance, parasite populations under sustained exposure to novel monoclonal hosts experienced rapid fitness increases evidenced by increased transmission rates. This demonstrates rapid adaptation of chytrids to novel hosts and highlights their high evolutionary potential. In contrast, increased fitness was not detected in parasites exposed to multiclonal host mixtures, indicating that cyanobacterial intraspecific diversity hampers parasites adaptation. Significant increases in intensity of infection were observed in monoclonal and multiclonal treatments, suggesting high evolvability of traits involved in parasite attachment onto hosts (i.e., encystment). A comparison of the performance of evolved and unevolved (control) parasite populations against their common ancestral host did not reveal parasite attenuation. Our results exemplify the ability of chytrid parasites to adapt rapidly to new hosts, while providing experimental evidence that genetic diversity in host populations grants increased resistance to disease by hindering parasite adaptation.
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Affiliation(s)
- Ramsy Agha
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Alina Gross
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Thomas Rohrlack
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Justyna Wolinska
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
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