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Duque-Jaramillo A, Ulmer N, Alseekh S, Bezrukov I, Fernie AR, Skirycz A, Karasov TL, Weigel D. The genetic and physiological basis of Arabidopsis thaliana tolerance to Pseudomonas viridiflava. THE NEW PHYTOLOGIST 2023; 240:1961-1975. [PMID: 37667565 DOI: 10.1111/nph.19241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
The opportunistic pathogen Pseudomonas viridiflava colonizes > 50 agricultural crop species and is the most common Pseudomonas in the phyllosphere of European Arabidopsis thaliana populations. Belonging to the P. syringae complex, it is genetically and phenotypically distinct from well-characterized P. syringae sensu stricto. Despite its prevalence, we lack knowledge of how A. thaliana responds to its native isolates at the molecular level. Here, we characterize the host response in an A. thaliana - P. viridiflava pathosystem. We measured host and pathogen growth in axenic infections and used immune mutants, transcriptomics, and metabolomics to determine defense pathways influencing susceptibility to P. viridiflava infection. Infection with P. viridiflava increased jasmonic acid (JA) levels and the expression of ethylene defense pathway marker genes. The immune response in a susceptible host accession was delayed compared with a tolerant one. Mechanical injury rescued susceptibility, consistent with an involvement of JA. The JA/ethylene pathway is important for suppression of P. viridiflava, yet suppression capacity varies between accessions. Our results shed light on how A. thaliana can suppress the ever-present P. viridiflava, but further studies are needed to understand how P. viridiflava evades this suppression to spread broadly across A. thaliana populations.
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Affiliation(s)
| | - Nina Ulmer
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ilja Bezrukov
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Boyce Thompson Institute, Cornell University, Ithaca, 14850, USA
| | - Talia L Karasov
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- School of Biological Sciences, University of Utah, Salt Lake City, 84112, USA
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, 72074, Germany
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Fernández-Sanz AM, Rodicio MR, González AJ. Biochemical Diversity, Pathogenicity and Phylogenetic Analysis of Pseudomonas viridiflava from Bean and Weeds in Northern Spain. Microorganisms 2022; 10:1542. [PMID: 36013960 PMCID: PMC9412563 DOI: 10.3390/microorganisms10081542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Pseudomonas viridiflava was originally reported as a bean pathogen, and subsequently as a wide-host range pathogen affecting numerous plants species. In addition, several authors have reported the epiphytic presence of this bacterium in "non-host plants", which may act as reservoir of P. viridiflava and source of inoculum for crops. A new biotype of this bacterium, showing an atypical LOPAT profile, was found in Asturias, a Northern region of Spain, causing significant damage in beans, kiwifruit, lettuce, and Hebe. In order to investigate the involvement of weeds in bean disease, samples were collected from beans and weeds growing in the same fields. A total of 48 isolates of P. viridiflava were obtained, 39 from weeds and 9 from beans. 48% and 52% of them showed typical (L- O- P+ A- T+) and atypical (L+ O- P v A- T+) LOPAT profiles, and they displayed high biochemical diversity. Regarding virulence factors, the T-PAI and S-PAI pathogenicity islands were found in 29% and 70.8% of the isolates, 81.2% displayed pectinolytic activity on potato slices, and 59% of the weed isolates produced symptoms after inoculation on bean pods. A phylogenetic tree based on concatenated rpoD, gyrB, and gltA sequences separated the strains carrying S-PAI and T-PAI into different clusters, both containing isolates from beans and weeds, and pathogenic as well as non-pathogenic strains. Closely related strains were found in the two hosts, and more than half of the weed isolates proved to be pathogenic in beans. This is consistent with the role of weeds as a reservoir and source of inoculum for bean infection. Detection of P. viridiflava in weeds throughout the year further supports these roles.
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Affiliation(s)
- Ana M. Fernández-Sanz
- Programa de Patología Vegetal, Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra AS-267, PK 19, 33300 Villaviciosa, Spain;
| | - M. Rosario Rodicio
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo, Julián Clavería 6, 33006 Oviedo, Spain;
| | - Ana J. González
- Programa de Patología Vegetal, Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra AS-267, PK 19, 33300 Villaviciosa, Spain;
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Lipps SM, Samac DA. Pseudomonas viridiflava: An internal outsider of the Pseudomonas syringae species complex. MOLECULAR PLANT PATHOLOGY 2022; 23:3-15. [PMID: 34463014 PMCID: PMC8659605 DOI: 10.1111/mpp.13133] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Pseudomonas viridiflava is a gram-negative pseudomonad that is phylogenetically placed within the Pseudomonas syringae species complex. P. viridiflava has a wide host range and causes a variety of symptoms in different plant parts, including stems, leaves, and blossoms. Outside of its role as a pathogen, P. viridiflava also exists as an endophyte, epiphyte, and saprophyte. Increased reports of P. viridiflava causing disease on new hosts in recent years coincide with increased research on its genetic variability, virulence, phylogenetics, and phenotypes. There is high variation in its core genome, virulence factors, and phenotypic characteristics. The main virulence factors of this pathogen include the enzyme pectate lyase and virulence genes encoded within one or two pathogenicity islands. The delineation of P. viridiflava in the P. syringae complex has been investigated using several molecular approaches. P. viridiflava comprises its own species, within the complex. While seemingly an outsider to the complex as a whole due to differences in the core genome and virulence genes, low average nucleotide identity to other of P. syringae complex members, and some phenotypic traits, it remains as part of the complex. Defining phylogenetic, phenotypic, and genomic characteristics of P. viridiflava in comparison to other P. syringae members is important to understanding this pathogen and for the development of disease resistance and management practices. TAXONOMY Kingdom Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Family Pseudomonadaceae; Genus Pseudomonas; Species Pseudomonas syringae species complex, Genomospecies 6, Phylogroup 7 and 8. MICROBIOLOGICAL PROPERTIES Gram-negative, fluorescent, aerobic, motile, rod-shaped, oxidase negative, arginine dihydrolase negative, levan production negative (or positive), potato rot positive (or negative), tobacco hypersensitivity positive. GENOME There are two complete genomes, five chromosome-level genomes, and 1,540 genomes composed of multiple scaffolds of P. viridiflava available in the National Center for Biotechnology Information Genome database. The median total length of these assemblies is 5,975,050 bp, the median number of protein coding genes is 5,208, and the median G + C content is 59.3%. DISEASE SYMPTOMS P. viridiflava causes a variety of disease symptoms, including spots, streaks, necrosis, rots, and more in above- and below-ground plant parts on at least 50 hosts. EPIDEMIOLOGY There have been several significant disease outbreaks on field and horticultural crops caused by P. viridiflava since the turn of the century. P. viridiflava has been reported as a pathogen, epiphyte, endophyte, and saprophyte. This species has been isolated from a variety of environmental sources, including asymptomatic wild plants, snow, epilithic biofilms, and icepacks.
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Affiliation(s)
- Savana M. Lipps
- Plant PathologyUniversity of Minnesota Twin CitiesSt PaulMNUSA
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Bophela KN, Petersen Y, Bull CT, Coutinho TA. Identification of Pseudomonas Isolates Associated With Bacterial Canker of Stone Fruit Trees in the Western Cape, South Africa. PLANT DISEASE 2020; 104:882-892. [PMID: 31935341 DOI: 10.1094/pdis-05-19-1102-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial canker is a common bacterial disease of stone fruit trees. The causal agents responsible for the disease include several pathovars in Pseudomonas syringae sensu lato and newly described Pseudomonas species. Pseudomonad strains were isolated from symptomatic stone fruit trees, namely apricot, peach, and plum trees cultivated in spatially separated orchards in the Western Cape. A polyphasic approach was used to identify and characterize these strains. Using a multilocus sequence typing approach of four housekeeping loci, namely cts, gapA, gyrB, and rpoD, the pseudomonad strains were delineated into two phylogenetic groups within P. syringae sensu lato: P. syringae sensu stricto and Pseudomonas viridiflava. These results were further supported by LOPAT diagnostic assays and analysis of clades in the rep-PCR dendrogram. The pseudomonad strains were pathogenic on both apricot and plum seedlings, indicative of a lack of host specificity between Pseudomonas strains infecting Prunus spp. This is a first report of P. viridiflava isolated from plum trees showing symptoms of bacterial canker. P. viridiflava is considered to be an opportunistic pathogen that causes foliar diseases of vegetable crops, fruit trees, and aromatic herbs, and thus the isolation of pathogenic P. viridiflava from twigs of plum trees showing symptoms of bacterial canker suggests that this bacterial species is a potentially emerging stem canker pathogen of stone fruit trees in South Africa.
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Affiliation(s)
- Khumbuzile N Bophela
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield 0028, Pretoria, South Africa
| | - Yolanda Petersen
- Crop Development Division, Agricultural Research Council, Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA 16801, U.S.A
| | - Teresa A Coutinho
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield 0028, Pretoria, South Africa
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5
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Cheng F, Ma A, Luo J, Zhuang X, Zhuang G. N-acylhomoserine lactone-regulation of genes mediating motility and pathogenicity in Pseudomonas syringae pathovar tabaci 11528. Microbiologyopen 2017; 6:e00440. [PMID: 28133926 PMCID: PMC5458577 DOI: 10.1002/mbo3.440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/28/2016] [Accepted: 12/07/2016] [Indexed: 11/11/2022] Open
Abstract
Pseudomonas syringae pathovar tabaci 11528 (P. syringae 11528) is a phytopathogen that causes wild-fire disease in soybean and tobacco plants. It utilizes a cell density-dependent regulation system known as quorum sensing (QS). In its QS system, the psyI is responsible for the biosynthesis of N-acylhomoserine lactones (AHLs). By comparing the transcripts from P. syringae 11528 wild-type strain with those of the ΔpsyI mutant using RNA sequencing (RNA-seq) technology, 1118 AHL-regulated genes were identified in the transition from exponential to stationary growth phase. Numerous AHL-regulated genes involved in pathogenicity were negatively controlled, including genes linked to flagella, chemotaxis, pilus, extracellular polysaccharides, secretion systems, and two-component system. Moreover, gene ontology and pathway enrichment analysis revealed that the most pronounced regulation was associated with bacterial motility. Finally, phenotypic assays showed that QS-regulated traits were involved in epiphytic growth of pathogens and disease development in plants. These findings imply that the AHL-mediated QS system in P. syringae 11528 plays significant roles in distinct stages of interactions between plants and pathogens, including early plant colonization and late plant infection.
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Affiliation(s)
- Feifei Cheng
- Research Center for Eco‐Environment SciencesChinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Anzhou Ma
- Research Center for Eco‐Environment SciencesChinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Jinxue Luo
- Research Center for Eco‐Environment SciencesChinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Xuliang Zhuang
- Research Center for Eco‐Environment SciencesChinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Guoqiang Zhuang
- Research Center for Eco‐Environment SciencesChinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
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Rossi FR, Marina M, Pieckenstain FL. Role of Arginine decarboxylase (ADC) in Arabidopsis thaliana defence against the pathogenic bacterium Pseudomonas viridiflava. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:831-9. [PMID: 25409942 DOI: 10.1111/plb.12289] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 11/12/2014] [Indexed: 05/26/2023]
Abstract
Polyamine biosynthesis starts with putrescine production through the decarboxylation of arginine or ornithine. In Arabidopsis thaliana, putrescine is synthesised exclusively by arginine decarboxylase (ADC), which exists as two isoforms (ADC1 and 2) that are differentially regulated by abiotic stimuli, but their role in defence against pathogens has not been studied in depth. This work analysed the participation of ADC in Arabidopsis defence against Pseudomonas viridiflava. ADC activity and expression, polyamine levels and bacterial resistance were analysed in null mutants of each ADC isoform. In non-infected wild-type (WT) plants, ADC2 expression was much higher than ADC1. Analysis of adc mutants demonstrated that ADC2 contributes to a much higher extent than ADC1 to basal ADC activity and putrescine biosynthesis. In addition, adc2 mutants showed increased basal expression of salicylic acid- and jasmonic acid-dependent PR genes. Bacterial infection induced putrescine accumulation and ADC1 expression in WT plants, but pathogen-induced putrescine accumulation was blocked in adc1 mutants. Results suggest a specific participation of ADC1 in defence, although basal resistance was not decreased by dysfunction of either of the two ADC genes. In addition, and as opposed to WT plants, bacterial infection increased ADC2 expression and ADC activity in adc1 mutants, which could counterbalance the lack of ADC1. Results demonstrate a major contribution of ADC2 to total ADC activity and the specific induction of ADC1 in response to infection. A certain degree of functional redundancy between the two isoforms in relation to their contribution to basal resistance is also evident.
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Affiliation(s)
- F R Rossi
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús, Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - M Marina
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús, Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - F L Pieckenstain
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús, Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
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7
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Schleker S, Kshirsagar M, Klein-Seetharaman J. Comparing human-Salmonella with plant-Salmonella protein-protein interaction predictions. Front Microbiol 2015; 6:45. [PMID: 25674082 PMCID: PMC4309195 DOI: 10.3389/fmicb.2015.00045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 01/13/2015] [Indexed: 11/13/2022] Open
Abstract
Salmonellosis is the most frequent foodborne disease worldwide and can be transmitted to humans by a variety of routes, especially via animal and plant products. Salmonella bacteria are believed to use not only animal and human but also plant hosts despite their evolutionary distance. This raises the question if Salmonella employs similar mechanisms in infection of these diverse hosts. Given that most of our understanding comes from its interaction with human hosts, we investigate here to what degree knowledge of Salmonella-human interactions can be transferred to the Salmonella-plant system. Reviewed are recent publications on analysis and prediction of Salmonella-host interactomes. Putative protein-protein interactions (PPIs) between Salmonella and its human and Arabidopsis hosts were retrieved utilizing purely interolog-based approaches in which predictions were inferred based on available sequence and domain information of known PPIs, and machine learning approaches that integrate a larger set of useful information from different sources. Transfer learning is an especially suitable machine learning technique to predict plant host targets from the knowledge of human host targets. A comparison of the prediction results with transcriptomic data shows a clear overlap between the host proteins predicted to be targeted by PPIs and their gene ontology enrichment in both host species and regulation of gene expression. In particular, the cellular processes Salmonella interferes with in plants and humans are catabolic processes. The details of how these processes are targeted, however, are quite different between the two organisms, as expected based on their evolutionary and habitat differences. Possible implications of this observation on evolution of host-pathogen communication are discussed.
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Affiliation(s)
- Sylvia Schleker
- Klein-Seetharaman Laboratory, Division of Metabolic and Vascular Health, Warwick Medical School, University of Warwick , Coventry, UK ; Department of Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn , Bonn, Germany
| | - Meghana Kshirsagar
- Language Technologies Institute, School of Computer Science, Carnegie Mellon University , Pittsburgh, PA, USA
| | - Judith Klein-Seetharaman
- Klein-Seetharaman Laboratory, Division of Metabolic and Vascular Health, Warwick Medical School, University of Warwick , Coventry, UK
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8
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Salicylic Acid Signaling in Plant Innate Immunity. PLANT HORMONE SIGNALING SYSTEMS IN PLANT INNATE IMMUNITY 2015. [DOI: 10.1007/978-94-017-9285-1_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Trujillo ME, Bacigalupe R, Pujic P, Igarashi Y, Benito P, Riesco R, Médigue C, Normand P. Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style? PLoS One 2014; 9:e108522. [PMID: 25268993 PMCID: PMC4182475 DOI: 10.1371/journal.pone.0108522] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/22/2014] [Indexed: 12/03/2022] Open
Abstract
Endophytic microorganisms live inside plants for at least part of their life cycle. According to their life strategies, bacterial endophytes can be classified as “obligate” or “facultative”. Reports that members of the genus Micromonospora, Gram-positive Actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestrial to a facultative endophytic life. The aim of this work was to analyse the genome sequence of Micromonospora lupini Lupac 08 isolated from a nitrogen fixing nodule of the legume Lupinus angustifolius and to identify genomic traits that provide information on this new plant-microbe interaction. The genome of M. lupini contains a diverse array of genes that may help its survival in soil or in plant tissues, while the high number of putative plant degrading enzyme genes identified is quite surprising since this bacterium is not considered a plant-pathogen. Functionality of several of these genes was demonstrated in vitro, showing that Lupac 08 degraded carboxymethylcellulose, starch and xylan. In addition, the production of chitinases detected in vitro, indicates that strain Lupac 08 may also confer protection to the plant. Micromonospora species appears as new candidates in plant-microbe interactions with an important potential in agriculture and biotechnology. The current data strongly suggests that a beneficial effect is produced on the host-plant.
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Affiliation(s)
- Martha E. Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
- * E-mail:
| | - Rodrigo Bacigalupe
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Petar Pujic
- Université Lyon 1, Université de Lyon, CNRS-UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, Kurokawa, Imizu, Toyama, Japan
| | - Patricia Benito
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Claudine Médigue
- Genoscope, CNRS-UMR 8030, Atelier de Génomique Comparative, Evry, France
| | - Philippe Normand
- Université Lyon 1, Université de Lyon, CNRS-UMR5557 Ecologie Microbienne, Villeurbanne, France
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Bartoli C, Berge O, Monteil CL, Guilbaud C, Balestra GM, Varvaro L, Jones C, Dangl JL, Baltrus DA, Sands DC, Morris CE. ThePseudomonas viridiflavaphylogroups in theP. syringaespecies complex are characterized by genetic variability and phenotypic plasticity of pathogenicity-related traits. Environ Microbiol 2014; 16:2301-15. [DOI: 10.1111/1462-2920.12433] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 02/13/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Claudia Bartoli
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE); Tuscia University; Viterbo Italy
- UR0407 Pathologie Végétale; INRA; Montfavet France
| | - Odile Berge
- UR0407 Pathologie Végétale; INRA; Montfavet France
| | | | | | - Giorgio M. Balestra
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE); Tuscia University; Viterbo Italy
| | - Leonardo Varvaro
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE); Tuscia University; Viterbo Italy
| | - Corbin Jones
- Department of Biology; Carolina Center for Genome Sciences; Chapel Hill NC 29599 USA
| | - Jeffery L. Dangl
- Department of Biology; Howard Hughes Medical Institute; University of North Carolina; Chapel Hill NC 29599 USA
| | - David A. Baltrus
- School of Plant Sciences; University of Arizona; Tucson AZ 85721 USA
| | - David C. Sands
- Department Plant Sciences and Plant Pathology; Montana State University; Bozeman MT 59717-3150 USA
| | - Cindy E. Morris
- UR0407 Pathologie Végétale; INRA; Montfavet France
- Department Plant Sciences and Plant Pathology; Montana State University; Bozeman MT 59717-3150 USA
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11
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Schwachtje J, Karojet S, Kunz S, Brouwer S, van Dongen JT. Plant-growth promoting effect of newly isolated rhizobacteria varies between two Arabidopsis ecotypes. PLANT SIGNALING & BEHAVIOR 2012; 7:623-7. [PMID: 22580689 PMCID: PMC3442855 DOI: 10.4161/psb.20176] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Various rhizobacteria are known for their beneficial effects on plants, i. e. promotion of growth and induction of systemic resistance against pathogens. These bacteria are categorized as plant growth promoting rhizobacteria (PGPR) and are associated with plant roots. Knowledge of the underlying mechanisms of plant growth promotion in vivo is still very limited, but interference of bacteria with plant hormone metabolism is suggested to play a major role. To obtain new growth promoting bacteria, we started a quest for rhizobacteria that are naturally associated to Arabidopsis thaliana. A suite of native root-associated bacteria were isolated from surface-sterilized roots of the Arabidopsis ecotype Gol-1 derived from a field site near Golm (Berlin area, Germany). We found several Pseudomonas and a Microbacterium species and tested these for growth promotion effects on the Arabidopsis ecotypes Gol-1 and Col-0, and for growth-promotion associated traits, such as auxin production, ACC deaminase activity and phosphate solubilization capacity. We showed that two of the bacteria strains promote plant growth with respect to rosette diameter, stalk length and accelerate development and that the effects were greater when bacteria were applied to Col-0 compared with Gol-1. Furthermore, the capability of promoting growth was not explained by the tested metabolic properties of the bacteria, suggesting that further bacterial traits are required. The natural variation of growth effects, combined with the extensive transgenic approaches available for the model plant Arabidopsis, will build a valuable tool to augment our understanding of the molecular mechanisms involved in the natural Arabidopsis - PGPR association.
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Affiliation(s)
- Jens Schwachtje
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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12
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Schwachtje J, Karojet S, Thormählen I, Bernholz C, Kunz S, Brouwer S, Schwochow M, Köhl K, van Dongen JT. A naturally associated rhizobacterium of Arabidopsis thaliana induces a starvation-like transcriptional response while promoting growth. PLoS One 2011; 6:e29382. [PMID: 22216267 PMCID: PMC3247267 DOI: 10.1371/journal.pone.0029382] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 11/28/2011] [Indexed: 12/29/2022] Open
Abstract
Plant growth promotion by rhizobacteria is a known phenomenon but the underlying mechanisms are poorly understood. We searched for plant growth-promoting rhizobacteria that are naturally associated with Arabidopsis thaliana to investigate the molecular mechanisms that are involved in plant growth-promotion. We isolated a Pseudomonas bacterium (Pseudomonas sp. G62) from roots of field-grown Arabidopsis plants that has not been described previously and analyzed its effect on plant growth, gene expression and the level of sugars and amino acids in the host plant. Inoculation with Pseudomonas sp. G62 promoted plant growth under various growth conditions. Microarray analysis revealed rapid changes in transcript levels of genes annotated to energy-, sugar- and cell wall metabolism in plants 6 h after root inoculation with P. sp. G62. The expression of several of these genes remained stable over weeks, but appeared differentially regulated in roots and shoots. The global gene expression profile observed after inoculation with P. sp. G62 showed a striking resemblance with previously described carbohydrate starvation experiments, although plants were not depleted from soluble sugars, and even showed a slight increase of the sucrose level in roots 5 weeks after inoculation. We suggest that the starvation-like transcriptional phenotype - while steady state sucrose levels are not reduced - is induced by a yet unknown signal from the bacterium that simulates sugar starvation. We discuss the potential effects of the sugar starvation signal on plant growth promotion.
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Affiliation(s)
- Jens Schwachtje
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- * E-mail: (JS); (JTvD)
| | - Silke Karojet
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ina Thormählen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Carolin Bernholz
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Sabine Kunz
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Stephan Brouwer
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Melanie Schwochow
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Karin Köhl
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Joost T. van Dongen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- * E-mail: (JS); (JTvD)
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13
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Barrett LG, Bell T, Dwyer G, Bergelson J. Cheating, trade-offs and the evolution of aggressiveness in a natural pathogen population. Ecol Lett 2011; 14:1149-57. [PMID: 21951910 DOI: 10.1111/j.1461-0248.2011.01687.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The evolutionary dynamics of pathogens are critically important for disease outcomes, prevalence and emergence. In this study we investigate ecological conditions that may promote the long-term maintenance of virulence polymorphisms in pathogen populations. Recent theory predicts that evolution towards increased virulence can be reversed if less-aggressive social 'cheats' exploit more aggressive 'cooperator' pathogens. However, there is no evidence that social exploitation operates within natural pathogen populations. We show that for the bacterium Pseudomonas syringae, major polymorphisms for pathogenicity are maintained at unexpectedly high frequencies in populations infecting the host Arabidopsis thaliana. Experiments reveal that less-aggressive strains substantially increase their growth potential in mixed infections and have a fitness advantage in non-host environments. These results suggest that niche differentiation can contribute to the maintenance of virulence polymorphisms, and that both within-host and between-host growth rates modulate cheating and cooperation in P. syringae populations.
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Affiliation(s)
- Luke G Barrett
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, USA
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14
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Curvers K, Seifi H, Mouille G, de Rycke R, Asselbergh B, Van Hecke A, Vanderschaeghe D, Höfte H, Callewaert N, Van Breusegem F, Höfte M. Abscisic acid deficiency causes changes in cuticle permeability and pectin composition that influence tomato resistance to Botrytis cinerea. PLANT PHYSIOLOGY 2010; 154:847-60. [PMID: 20709830 PMCID: PMC2949027 DOI: 10.1104/pp.110.158972] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 08/08/2010] [Indexed: 05/19/2023]
Abstract
A mutant of tomato (Solanum lycopersicum) with reduced abscisic acid (ABA) production (sitiens) exhibits increased resistance to the necrotrophic fungus Botrytis cinerea. This resistance is correlated with a rapid and strong hydrogen peroxide-driven cell wall fortification response in epidermis cells that is absent in tomato with normal ABA production. Moreover, basal expression of defense genes is higher in the mutant compared with the wild-type tomato. Given the importance of this fast response in sitiens resistance, we investigated cell wall and cuticle properties of the mutant at the chemical, histological, and ultrastructural levels. We demonstrate that ABA deficiency in the mutant leads to increased cuticle permeability, which is positively correlated with disease resistance. Furthermore, perturbation of ABA levels affects pectin composition. sitiens plants have a relatively higher degree of pectin methylesterification and release different oligosaccharides upon inoculation with B. cinerea. These results show that endogenous plant ABA levels affect the composition of the tomato cuticle and cell wall and demonstrate the importance of cuticle and cell wall chemistry in shaping the outcome of this plant-fungus interaction.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Monica Höfte
- Laboratory of Phytopathology (K.C., H.S., B.A., M.H.) and Department of Plant Biotechnology and Genetics (K.C., R.d.R., F.V.B.), Ghent University, B–9000 Ghent, Belgium; Department of Plant Systems Biology (K.C., R.d.R., F.V.B.) and Department for Molecular Biomedical Research (A.V.H., D.V., N.C.), VIB, B–9052 Ghent, Belgium; Plate-forme de Chimie du Végétal, Institut Jean-Pierre Bourgin, UMR1318, Institut National de la Recherche Agronomique, 78026 Versailles cedex, France (G.M., H.H.); Department of Molecular Genetics, Flanders Institute for Biotechnology, B–2660 Wilrijk, Belgium (B.A.)
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15
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Studholme DJ, Ibanez SG, MacLean D, Dangl JL, Chang JH, Rathjen JP. A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528. BMC Genomics 2009; 10:395. [PMID: 19703286 PMCID: PMC2745422 DOI: 10.1186/1471-2164-10-395] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 08/24/2009] [Indexed: 11/28/2022] Open
Abstract
Background Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is dependent on the type III secretion system, which secretes a suite of up to about thirty virulence 'effector' proteins into the host cytoplasm where they subvert the eukaryotic cell physiology and disrupt host defences. P. syringae pathovar tabaci naturally causes disease on wild tobacco, the model member of the Solanaceae, a family that includes many crop species as well as on soybean. Results We used the 'next-generation' Illumina sequencing platform and the Velvet short-read assembly program to generate a 145X deep 6,077,921 nucleotide draft genome sequence for P. syringae pathovar tabaci strain 11528. From our draft assembly, we predicted 5,300 potential genes encoding proteins of at least 100 amino acids long, of which 303 (5.72%) had no significant sequence similarity to those encoded by the three previously fully sequenced P. syringae genomes. Of the core set of Hrp Outer Proteins that are conserved in three previously fully sequenced P. syringae strains, most were also conserved in strain 11528, including AvrE1, HopAH2, HopAJ2, HopAK1, HopAN1, HopI, HopJ1, HopX1, HrpK1 and HrpW1. However, the hrpZ1 gene is partially deleted and hopAF1 is completely absent in 11528. The draft genome of strain 11528 also encodes close homologues of HopO1, HopT1, HopAH1, HopR1, HopV1, HopAG1, HopAS1, HopAE1, HopAR1, HopF1, and HopW1 and a degenerate HopM1'. Using a functional screen, we confirmed that hopO1, hopT1, hopAH1, hopM1', hopAE1, hopAR1, and hopAI1' are part of the virulence-associated HrpL regulon, though the hopAI1' and hopM1' sequences were degenerate with premature stop codons. We also discovered two additional HrpL-regulated effector candidates and an HrpL-regulated distant homologue of avrPto1. Conclusion The draft genome sequence facilitates the continued development of P. syringae pathovar tabaci on wild tobacco as an attractive model system for studying bacterial disease on plants. The catalogue of effectors sheds further light on the evolution of pathogenicity and host-specificity as well as providing a set of molecular tools for the study of plant defence mechanisms. We also discovered several large genomic regions in Pta 11528 that do not share detectable nucleotide sequence similarity with previously sequenced Pseudomonas genomes. These regions may include horizontally acquired islands that possibly contribute to pathogenicity or epiphytic fitness of Pta 11528.
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16
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Cantu D, Vicente AR, Labavitch JM, Bennett AB, Powell ALT. Strangers in the matrix: plant cell walls and pathogen susceptibility. TRENDS IN PLANT SCIENCE 2008; 13:610-7. [PMID: 18824396 DOI: 10.1016/j.tplants.2008.09.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 08/29/2008] [Accepted: 09/03/2008] [Indexed: 05/04/2023]
Abstract
Early in infection, pathogens encounter the outer wall of plant cells. Because pathogen hydrolases targeting the plant cell wall are well-known components of virulence, it has been assumed that wall disassembly by the plant itself also contributes to susceptibility, and now this has been established experimentally. Understanding how plant morphological and developmental remodeling and pathogen cell wall targeted virulence influence infections provides new perspectives about plant-pathogen interactions. The plant cell wall can be an effective physical barrier to pathogens, but also it is a matrix where many proteins involved in pathogen perception are delivered. By breaching the wall, a pathogen potentially reveals itself to the plant and activates responses, setting off events that might halt or limit its advance.
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Affiliation(s)
- Dario Cantu
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
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17
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Kniskern JM, Traw MB, Bergelson J. Salicylic acid and jasmonic acid signaling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1512-22. [PMID: 17990959 DOI: 10.1094/mpmi-20-12-1512] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Terrestrial plants serve as large and diverse habitats for a wide range of pathogenic and nonpathogenic microbes, yet these communities are not well described and little is known about the effects of plant defense on microbial communities in nature. We designed a field experiment to determine how variation in two plant defense signaling pathways affects the size, diversity, and composition of the natural endophytic and epiphytic bacterial communities of Arabidopsis thaliana. To do this, we provide an initial characterization of these bacterial communities in one population in southwestern Michigan, United States, and we compare these two communities among A. thaliana mutants deficient in salicylic acid (SA) and jasmonic acid (JA) signaling defense pathways, controls, and plants with artificially elevated levels of defense. We identified 30 distinct bacterial groups on A. thaliana that differ in colony morphology and 16S rRNA sequence. We show that induction of SA-mediated defenses reduced endophytic bacterial community diversity, whereas plants deficient in JA-mediated defenses experienced greater epiphytic bacterial diversity. Furthermore, there was a positive relationship between total community size and diversity, indicating that relatively susceptible plants should, in general, harbor higher bacterial diversity. This experiment provides novel information about the ecology of bacteria on A. thaliana and demonstrates that variation in two specific plant-signaling defense pathways can influence bacterial diversity on plants.
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Affiliation(s)
- Joel M Kniskern
- Department of Ecology and Evolution, University of Chicago, 60637, USA
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18
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Traw MB, Kniskern JM, Bergelson J. SAR increases fitness of Arabidopsis thaliana in the presence of natural bacterial pathogens. Evolution 2007; 61:2444-9. [PMID: 17725640 DOI: 10.1111/j.1558-5646.2007.00211.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Given the substantial costs of plant defenses against pathogens, there should be corresponding benefits that prevent resistance from being lost in natural plant populations. Here, we present evidence that systemic acquired resistance (SAR) benefits plants attacked by pathogenic bacteria in nature. In a large field experiment, we found that Arabidopsis thaliana treated with salicylic acid exhibited reduced titers of bacteria in their leaves and elevated fitness relative to controls. Most common members of the culturable bacterial community suffered this decrease, consistent with the role of SAR as a broad spectrum defense. We found no evidence of negative interactions between SAR and jasmonate-dependent resistance. Plants treated with jasmonic acid received significantly lower insect damage to their siliques, but exhibited no differences in bacterial growth or fitness relative to controls. Collectively, these data suggest a likely role of pathogenic bacteria in the maintenance of SAR, but not jasmonate-dependent resistance, in nature.
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Affiliation(s)
- M Brian Traw
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
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19
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Araki H, Innan H, Kreitman M, Bergelson J. Molecular evolution of pathogenicity-island genes in Pseudomonas viridiflava. Genetics 2007; 177:1031-41. [PMID: 17720907 PMCID: PMC2034611 DOI: 10.1534/genetics.107.077925] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial pathogen Pseudomonas viridiflava possesses two pathogenicity islands (PAIs) that share many gene homologs, but are structurally and phenotypically differentiated (T-PAI and S-PAI). These PAIs are paralogous, but only one is present in each isolate. While this dual presence/absence polymorphism has been shown to be maintained by balancing selection, little is known about the molecular evolution of individual genes on the PAIs. Here we investigate genetic variation of 12 PAI gene loci (7 on T-PAI and 5 on S-PAI) in 96 worldwide isolates of P. viridiflava. These genes include avirulence genes (hopPsyA and avrE), their putative chaperones (shcA and avrF), and genes encoding the type III outer proteins (hrpA, hrpZ, and hrpW). Average nucleotide diversities in these genes (pi = 0.004-0.020) were close to those in the genetic background. Large numbers of recombination events were found within PAIs and a sign of positive selection was detected in avrE. These results suggest that the PAI genes are evolving relatively freely from each other on the PAIs, rather than as a single unit under balancing selection. Evolutionarily stable PAIs may be preferable in this species because preexisting genetic variation enables P. viridiflava to respond rapidly to natural selection.
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Affiliation(s)
- Hitoshi Araki
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.
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20
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Goss EM, Bergelson J. Fitness consequences of infection of Arabidopsis thaliana with its natural bacterial pathogen Pseudomonas viridiflava. Oecologia 2006; 152:71-81. [PMID: 17180370 DOI: 10.1007/s00442-006-0631-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 11/21/2006] [Indexed: 11/27/2022]
Abstract
Variation in plant resistance to pathogen infection is commonly observed in interactions between wild plants and their foliar pathogens. Models of host-pathogen interactions indicate that a large cost of infection is generally necessary to maintain this variation, yet there is limited evidence that foliar pathogens cause detectable fitness reductions in wild host plants. Most published work has focused on fungal pathogens. Pseudomonas viridiflava, a common bacterial pathogen of the annual weed Arabidopsis thaliana across its range, comprises two distinct genetic clades that cause disease symptoms of different severity. Here we measured the extent of infection of wild A. thaliana populations in the Midwest, USA, and examined the effect on seed production, in field and growth-chamber experiments, of experimental inoculation with isolates from the two clades. We found infection with P. viridiflava varied from 0 to 56% in Midwest A. thaliana populations, with the possibility of several leaves per plant infected later in the growing season. In the growth chambers, experimental inoculation reduced seed set by averages of 15 and 11% for clades A and B, respectively. In the field experiment, only clade A affected plant fitness significantly, reducing seed set by an average of 38%. Underlying these average effects we observed both negative and positive effects of infection, and variation in both fitness among plant genotypes and sensitivity to environmental conditions.
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Affiliation(s)
- Erica M Goss
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA.
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