Phenotypic and Molecular-Phylogenetic Analyses Reveal Distinct Features of Crown Gall-Associated Xanthomonas Strains

ABSTRACT In summer 2019, widespread occurrence of crown gall disease caused by Agrobacterium spp. was observed on commercially grown ornamental plants in southern Iran. Beside agrobacteria, pale yellow-pigmented Gram-negative strains resembling the members of Xanthomonas were also associated with cr...

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Main Authors: Hamzeh Mafakheri, S. Mohsen Taghavi, Sadegh Zarei, Touraj Rahimi, Mohammad Sadegh Hasannezhad, Perrine Portier, Marion Fischer-Le Saux, Ivica Dimkić, Ralf Koebnik, Nemanja Kuzmanović, Ebrahim Osdaghi
Format: Article
Language:English
Published: American Society for Microbiology 2022-02-01
Series:Microbiology Spectrum
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Online Access:https://journals.asm.org/doi/10.1128/spectrum.00577-21
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author Hamzeh Mafakheri
S. Mohsen Taghavi
Sadegh Zarei
Touraj Rahimi
Mohammad Sadegh Hasannezhad
Perrine Portier
Marion Fischer-Le Saux
Ivica Dimkić
Ralf Koebnik
Nemanja Kuzmanović
Ebrahim Osdaghi
author_facet Hamzeh Mafakheri
S. Mohsen Taghavi
Sadegh Zarei
Touraj Rahimi
Mohammad Sadegh Hasannezhad
Perrine Portier
Marion Fischer-Le Saux
Ivica Dimkić
Ralf Koebnik
Nemanja Kuzmanović
Ebrahim Osdaghi
author_sort Hamzeh Mafakheri
collection DOAJ
description ABSTRACT In summer 2019, widespread occurrence of crown gall disease caused by Agrobacterium spp. was observed on commercially grown ornamental plants in southern Iran. Beside agrobacteria, pale yellow-pigmented Gram-negative strains resembling the members of Xanthomonas were also associated with crown gall tissues on weeping fig (Ficus benjamina) and Amaranthus sp. plants. The purpose of the present study was to characterize the crown gall-associated Xanthomonas strains using plant inoculation assays, molecular-phylogenetic analyses, and comparative genomics approaches. Pathogenicity tests showed that the Xanthomonas strains did not induce disease symptoms on their host of isolation. However, the strains induced hypersensitive reaction on tobacco, geranium, melon, squash, and tomato leaves via leaf infiltration. Multilocus sequence analysis suggested that the strains belong to clade IA of Xanthomonas, phylogenetically close to Xanthomonas translucens, X. theicola, and X. hyacinthi. Average nucleotide identity and digital DNA-DNA hybridization values between the whole-genome sequences of the strains isolated in this study and reference Xanthomonas strains are far below the accepted thresholds for the definition of prokaryotic species, signifying that these strains could be defined as two new species within clade IA of Xanthomonas. Comparative genomics showed that the strains isolated from crown gall tissues are genetically distinct from X. translucens, as almost all the type III secretion system genes and type III effectors are lacking in the former group. The data obtained in this study provide novel insight into the breadth of genetic diversity of crown gall-associated bacteria and pave the way for research on gall-associated Xanthomonas-plant interactions. IMPORTANCE Tumorigenic agrobacteria—members of the bacterial family Rhizobiaceae—cause crown gall and hairy root diseases on a broad range of plant species. These bacteria are responsible for economic losses in nurseries of important fruit trees and ornamental plants. The microclimate of crown gall and their accompanying microorganisms has rarely been studied for the microbial diversity and population dynamics of gall-associated bacteria. Here, we employed a series of biochemical tests, pathogenicity assays, and molecular-phylogenetic analyses, supplemented with comparative genomics, to elucidate the biological features, taxonomic position, and genomic repertories of five crown gall-associated Xanthomonas strains isolated from weeping fig and Amaranthus sp. plants in Iran. The strains investigated in this study induced hypersensitive reactions (HR) on geranium, melon, squash, tobacco, and tomato leaves, while they were nonpathogenic on their host of isolation. Phylogenetic analyses and whole-genome-sequence-based average nucleotide identity (ANI)/digital DNA-DNA hybridization (dDDH) calculations suggested that the Xanthomonas strains isolated from crown gall tissues belong to two taxonomically unique clades closely related to the clade IA species of the genus, i.e., X. translucens, X. hyacinthi, and X. theicola.
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spelling doaj.art-95032fa6f9ec4acdb3ebcd9584de1c752022-12-21T16:58:27ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972022-02-0110110.1128/spectrum.00577-21Phenotypic and Molecular-Phylogenetic Analyses Reveal Distinct Features of Crown Gall-Associated Xanthomonas StrainsHamzeh Mafakheri0S. Mohsen Taghavi1Sadegh Zarei2Touraj Rahimi3Mohammad Sadegh Hasannezhad4Perrine Portier5Marion Fischer-Le Saux6Ivica Dimkić7Ralf Koebnik8Nemanja Kuzmanović9Ebrahim Osdaghi10Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, IranDepartment of Plant Protection, School of Agriculture, Shiraz University, Shiraz, IranDepartment of Plant Protection, School of Agriculture, Shiraz University, Shiraz, IranDepartment Plant Production and Genetics, Agriculture Faculty, Shahr-e-Qods Branch, Islamic Azad University, Tehran, IranUniversity of Applied Science and Technology, Sadra, IranUniversité Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, Angers, FranceUniversité Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, Angers, FranceDepartment of Biochemistry and Molecular Biology, University of Belgrade Faculty of Biology, Belgrade, SerbiaPlant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, FranceJulius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, GermanyDepartment of Plant Protection, College of Agriculture, University of Tehran, Karaj, IranABSTRACT In summer 2019, widespread occurrence of crown gall disease caused by Agrobacterium spp. was observed on commercially grown ornamental plants in southern Iran. Beside agrobacteria, pale yellow-pigmented Gram-negative strains resembling the members of Xanthomonas were also associated with crown gall tissues on weeping fig (Ficus benjamina) and Amaranthus sp. plants. The purpose of the present study was to characterize the crown gall-associated Xanthomonas strains using plant inoculation assays, molecular-phylogenetic analyses, and comparative genomics approaches. Pathogenicity tests showed that the Xanthomonas strains did not induce disease symptoms on their host of isolation. However, the strains induced hypersensitive reaction on tobacco, geranium, melon, squash, and tomato leaves via leaf infiltration. Multilocus sequence analysis suggested that the strains belong to clade IA of Xanthomonas, phylogenetically close to Xanthomonas translucens, X. theicola, and X. hyacinthi. Average nucleotide identity and digital DNA-DNA hybridization values between the whole-genome sequences of the strains isolated in this study and reference Xanthomonas strains are far below the accepted thresholds for the definition of prokaryotic species, signifying that these strains could be defined as two new species within clade IA of Xanthomonas. Comparative genomics showed that the strains isolated from crown gall tissues are genetically distinct from X. translucens, as almost all the type III secretion system genes and type III effectors are lacking in the former group. The data obtained in this study provide novel insight into the breadth of genetic diversity of crown gall-associated bacteria and pave the way for research on gall-associated Xanthomonas-plant interactions. IMPORTANCE Tumorigenic agrobacteria—members of the bacterial family Rhizobiaceae—cause crown gall and hairy root diseases on a broad range of plant species. These bacteria are responsible for economic losses in nurseries of important fruit trees and ornamental plants. The microclimate of crown gall and their accompanying microorganisms has rarely been studied for the microbial diversity and population dynamics of gall-associated bacteria. Here, we employed a series of biochemical tests, pathogenicity assays, and molecular-phylogenetic analyses, supplemented with comparative genomics, to elucidate the biological features, taxonomic position, and genomic repertories of five crown gall-associated Xanthomonas strains isolated from weeping fig and Amaranthus sp. plants in Iran. The strains investigated in this study induced hypersensitive reactions (HR) on geranium, melon, squash, tobacco, and tomato leaves, while they were nonpathogenic on their host of isolation. Phylogenetic analyses and whole-genome-sequence-based average nucleotide identity (ANI)/digital DNA-DNA hybridization (dDDH) calculations suggested that the Xanthomonas strains isolated from crown gall tissues belong to two taxonomically unique clades closely related to the clade IA species of the genus, i.e., X. translucens, X. hyacinthi, and X. theicola.https://journals.asm.org/doi/10.1128/spectrum.00577-21Agrobacterium sp.Amaranthus sp.clade I XanthomonasFicus benjaminaT3SSweeping fig
spellingShingle Hamzeh Mafakheri
S. Mohsen Taghavi
Sadegh Zarei
Touraj Rahimi
Mohammad Sadegh Hasannezhad
Perrine Portier
Marion Fischer-Le Saux
Ivica Dimkić
Ralf Koebnik
Nemanja Kuzmanović
Ebrahim Osdaghi
Phenotypic and Molecular-Phylogenetic Analyses Reveal Distinct Features of Crown Gall-Associated Xanthomonas Strains
Microbiology Spectrum
Agrobacterium sp.
Amaranthus sp.
clade I Xanthomonas
Ficus benjamina
T3SS
weeping fig
title Phenotypic and Molecular-Phylogenetic Analyses Reveal Distinct Features of Crown Gall-Associated Xanthomonas Strains
title_full Phenotypic and Molecular-Phylogenetic Analyses Reveal Distinct Features of Crown Gall-Associated Xanthomonas Strains
title_fullStr Phenotypic and Molecular-Phylogenetic Analyses Reveal Distinct Features of Crown Gall-Associated Xanthomonas Strains
title_full_unstemmed Phenotypic and Molecular-Phylogenetic Analyses Reveal Distinct Features of Crown Gall-Associated Xanthomonas Strains
title_short Phenotypic and Molecular-Phylogenetic Analyses Reveal Distinct Features of Crown Gall-Associated Xanthomonas Strains
title_sort phenotypic and molecular phylogenetic analyses reveal distinct features of crown gall associated xanthomonas strains
topic Agrobacterium sp.
Amaranthus sp.
clade I Xanthomonas
Ficus benjamina
T3SS
weeping fig
url https://journals.asm.org/doi/10.1128/spectrum.00577-21
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