1
|
Osdaghi E, Taghavi SM, Hamidizade M, Kariminejhad M, Fazliarab A, Hajian Maleki H, Baeyen S, Taghouti G, Jacques MA, Van Vaerenbergh J, Portier P. Multiphasic investigations imply transfer of orange-/red-pigmented strains of the bean pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens to a new species as C. aurantiacum sp. nov., elevation of the poinsettia pathogen C. flaccumfaciens pv. poinsettiae to the species level as C. Poinsettiae sp. nov., and synonymy of C. albidum with C. citreum. Syst Appl Microbiol 2024; 47:126489. [PMID: 38325043 DOI: 10.1016/j.syapm.2024.126489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
Curtobacterium flaccumfaciens (Microbacteriaceae), a plant-pathogenic coryneform species includes five pathovars with valid names and a number of proposed - but unvalidated - new members. In this study, phenotypic features and DNA similarity indexes were investigated among all C. flaccumfaciens members. Results showed that the C. flaccumfaciens pv. poinsettiae strains causing bacterial canker of Euphorbia pulcherrima in the USA as well as the orange-/red-pigmented strains of C. flaccumfaciens pv. flaccumfaciens pathogenic on dry beans in Iran are too distinct from each other and from the type strain of the species to be considered members of C. flaccumfaciens. Hence, the latter two groups were elevated at the species level as C. poinsettiae sp. nov. (ATCC 9682T = CFBP 2403T = ICMP 2566T = LMG 3715T = NCPPB 854T as type strain), and C. aurantiacum sp. nov. (50RT = CFBP 8819T = ICMP 22071T as type strain). Within the emended species C. flaccumfaciens comb. nov., yellow-pigmented strains causing bacterial wilt of dry beans and those causing bacterial canker of Euphorbia pulcherrima in Europe were retained as C. flaccumfaciens pv. flaccumfaciens and C. flaccumfaciens pv. poinsettiae, respectively; while taxonomic position of the sugar beet pathogen C. flaccumfaciens pv. beticola ATCC BAA144PT was confirmed. The newly described onion pathogen C. allii was also reclassified as C. flaccumfaciens pv. allii with the pathotype strain LMG 32517PT. Furthermore, C. flaccumfaciens pv. basellae causing bacterial leaf spot of malabar spinach (Basella rubra) was transferred to C. citreum pv. basellae with ATCC BAA143PT as pathotype.
Collapse
Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran.
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Mozhde Hamidizade
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran; Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Mehdi Kariminejhad
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Amal Fazliarab
- Iranian Sugarcane Research and Training Institute (ISCRTI), Ahvaz, Khuzestan, Iran
| | - Habibeh Hajian Maleki
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Steve Baeyen
- Flanders' Research Institute for Agriculture, Fisheries and Food (ILVO), Unit Plant Sciences, EU Reference Laboratory for Plant Health - on bacteria, Burgemeester van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Geraldine Taghouti
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marie-Agnes Jacques
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Johan Van Vaerenbergh
- Flanders' Research Institute for Agriculture, Fisheries and Food (ILVO), Unit Plant Sciences, EU Reference Laboratory for Plant Health - on bacteria, Burgemeester van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Perrine Portier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France.
| |
Collapse
|
2
|
Arizala D, Arif M. Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri. Genome Biol Evol 2024; 16:evae032. [PMID: 38385549 PMCID: PMC10946231 DOI: 10.1093/gbe/evae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability, and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified 7 lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging from 43 bp to 119 kb and 36 bp to 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides (LPS), flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri's evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.
Collapse
Affiliation(s)
- Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| |
Collapse
|
3
|
Osdaghi E, Taghavi SM, Hamidizade M, Fazliarab A, Hajian Maleki H, Li X, Jacques MA, Portier P. Clavibacter lycopersici sp. nov.: a peach-colored actinobacterium isolated from symptomless tomato plant. Int J Syst Evol Microbiol 2023; 73. [PMID: 37737062 DOI: 10.1099/ijsem.0.006022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
In 2015, Gram-positive peach-coloured actinobacterial strains were isolated from symptomless tomato phyllosphere in Iran. Biochemical and physiological characteristics, as well as 16S rRNA phylogeny showed that the strains belong to Clavibacter sp., while they were non-pathogenic on the host of isolation, and morphologically distinct from the tomato pathogen C. michiganensis and other plant-associated bacteria. Multilocus sequence analysis of five housekeeping genes showed that the two peach-coloured strains CFBP 8615T (Tom532T) and CFBP 8616 (Tom495) were phylogenetically distinct from all validly described Clavibacter species. Whole genome sequence-based indices, i.e. average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH), showed that the two peach-colored strains share nearly 100 % orthoANI value with one another, while they differ from all validly described Clavibacter species with the orthoANI/dDDH values <93 % and <50 %, respectively. Thus, based on both phenotypic features and orthoANI/dDDH indices the peach-coloured strains could belong to a new species within Clavibacter. In this study, we provide a formal species description for the peach-coloured tomato-associated Clavibacter strains. Clavibacter lycopersici sp. nov. is proposed for the new species with Tom532T = CFBP 8615T = ICMP 22100T as type strain.
Collapse
Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Mozhde Hamidizade
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Amal Fazliarab
- Iranian Sugarcane Research and Training Institute (ISCRTI), Ahvaz, Khuzestan, Iran
| | - Habibeh Hajian Maleki
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Xiang Li
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - Marie-Agnes Jacques
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Perrine Portier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| |
Collapse
|
4
|
Jelušić A, Scortichini M, Marković S, Mitrović P, Iličić R, Stanković S, Popović Milovanović T. Phylogeographic Analysis of Soft-Rot-Causing Pectobacterium spp. Strains Obtained from Cabbage in Serbia. Microorganisms 2023; 11:2122. [PMID: 37630682 PMCID: PMC10458556 DOI: 10.3390/microorganisms11082122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The aim of this study was to establish a link between genetic diversity and the geographic origin of Pectobacterium strains belonging to three species-P. carotovorum, P. versatile, and P. odoriferum-isolated from cabbage in Serbia by comparing their sequences with those of strains sourced from different hosts and countries in Europe, Asia, and North America. Phylogeographic relatedness was reconstructed using the Templeton, Crandall, and Sing's (TCS) haplotype network based on concatenated sequences of the housekeeping genes dnaX, icdA, mdh, and proA, while pairwise genetic distances were computed by applying the p-distance model. The obtained TCS haplotype networks indicated the existence of high intra-species genetic diversity among strains of all three species, as reflected in the 0.2-2.3%, 0.2-2.5%, and 0.1-1.7% genetic distance ranges obtained for P. carotovorum, P. versatile, and P. odoriferum, respectively. Five new haplotypes (denoted as HPc1-HPc5) were detected among cabbage strains of P. carotovorum, while one new haplotype was identified for both P. versatile (HPv1) and P. odoriferum (HPo1). None of the TCS haplotype networks provided evidence of significant correlation between geographic origin and the determined haplotypes, i.e., the infection origin. However, as haplotype network results are affected by the availability of sequencing data in public databases for the used genes and the number of analyzed strains, these findings may also be influenced by small sample size.
Collapse
Affiliation(s)
- Aleksandra Jelušić
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, Serbia; (A.J.); (S.M.)
| | - Marco Scortichini
- Council for Agronomical Research and Economics (CREA), Research Centre for Olive, Fruit and Citrus Crops, Via di Fioranello, 52, I-00134 Roma, Italy;
| | - Sanja Marković
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, Serbia; (A.J.); (S.M.)
| | - Petar Mitrović
- Institute for Field and Vegetable Crops—National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
| | - Renata Iličić
- Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Slaviša Stanković
- Faculty of Biology, University of Belgrade, Studentski Trg 16, 11000 Belgrade, Serbia;
| | | |
Collapse
|
5
|
Osdaghi E, Robertson AE, Jackson-Ziems TA, Abachi H, Li X, Harveson RM. Clavibacter nebraskensis causing Goss's wilt of maize: Five decades of detaining the enemy in the New World. MOLECULAR PLANT PATHOLOGY 2023; 24:675-692. [PMID: 36116105 DOI: 10.1111/mpp.13268] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 06/11/2023]
Abstract
Goss's bacterial wilt and leaf blight of maize (Zea mays) caused by the gram-positive coryneform bacterium Clavibacter nebraskensis is an economically important disease in North America. C. nebraskensis is included within the high-risk list of quarantine pathogens by several plant protection organizations (EPPO code: CORBMI), hence it is under strict quarantine control around the world. The causal agent was reported for the first time on maize in Nebraska (USA) in 1969. After an outbreak during the 1970s, prevalence of the disease decreased in the 1980s to the early 2000s, before the disease resurged causing a serious threat to maize production in North America. The re-emergence of Goss's wilt in the corn belt of the United States led to several novel achievements in understanding the pathogen biology and disease control. In this review, we provide an updated overview of the pathogen taxonomy, biology, and epidemiology as well as management strategies of Goss's wilt disease. First, a taxonomic history of the pathogen is provided followed by symptomology and host range, genetic diversity, and pathogenicity mechanisms of the bacterium. Then, utility of high-throughput molecular approaches in the precise detection and identification of the pathogen and the management strategies of the disease are explained. Finally, we highlight the role of integrated pest management strategies to combat the risk of Goss's wilt in the 21st century maize industry. DISEASE SYMPTOMS Large (2-15 cm) tan to grey elongated oval lesions with wavy, irregular water-soaked margins on the leaves. The lesions often start at the leaf tip or are associated with wounding caused by hail or wind damage. Small (1 mm in diameter), dark, discontinuous water-soaked spots, known as "freckles", can be observed in the periphery of lesions. When backlit, the freckles appear translucent. Early infection (prior to growth stage V6) may become systemic and cause seedlings to wilt, wither, and die. Coalescence of lesions results in leaf blighting. HOST RANGE Maize (Zea mays) is the only economic host of the pathogen. A number of Poaceae species are reported to act as secondary hosts for C. nebraskensis. TAXONOMIC STATUS OF THE PATHOGEN Class: Actinobacteria; Order: Micrococcales; Family: Microbacteriaceae; Genus: Clavibacter; Species: Clavibacter nebraskensis. SYNONYMS Corynebacterium nebraskense (Schuster, 1970) Vidaver & Mandel 1974; Corynebacterium michiganense pv. nebraskense (Vidaver & Mandel 1974) Dye & Kemp 1977; Corynebacterium michiganense subsp. nebraskense (Vidaver & Mandel 1974) Carlson & Vidaver 1982; Clavibacter michiganense subsp. nebraskense (Vidaver & Mandel 1974) Davis et al. 1984; Clavibacter michiganensis subsp. nebraskensis (Vidaver & Mandel 1974) Davis et al. 1984. TYPE MATERIALS ATCC 27794T ; CFBP 2405T ; ICMP 3298T ; LMG 3700T ; NCPPB 2581T . MICROBIOLOGICAL PROPERTIES Cells are gram-positive, orange-pigmented, pleomorphic club- or rod-shaped, nonspore-forming, nonmotile, and without flagella, approximately 0.5 × 1-2.0 μm. DISTRIBUTION The pathogen is restricted to Canada and the United States. PHYTOSANITARY CATEGORIZATION EPPO code CORBNE.
Collapse
Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Alison E Robertson
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Tamra A Jackson-Ziems
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Hamid Abachi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Xiang Li
- Canadian Food Inspection Agency, Charlottetown Laboratory, Charlottetown, Prince Edward Island, Canada
| | - Robert M Harveson
- Panhandle Research & Extension Center, University of Nebraska, Scottsbluff, Nebraska, USA
| |
Collapse
|
6
|
Osdaghi E, van der Wolf JM, Abachi H, Li X, De Boer S, Ishimaru CA. Bacterial ring rot of potato caused by Clavibacter sepedonicus: A successful example of defeating the enemy under international regulations. MOLECULAR PLANT PATHOLOGY 2022; 23:911-932. [PMID: 35142424 PMCID: PMC9190974 DOI: 10.1111/mpp.13191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bacterial ring rot of potato (Solanum tuberosum) caused by the gram-positive coryneform bacterium Clavibacter sepedonicus is an important quarantine disease threatening the potato industry around the globe. Since its original description in 1906 in Germany, management of ring rot has been a major problem due to the seedborne nature (via seed tubers not true seeds) of the pathogen allowing the bacterium to be transmitted long distances via infected tubers. DISEASE SYMPTOMS On growing potato plants: interveinal chlorosis on leaflets leading to necrotic areas and systemic wilt. On infected tubers: vascular tissues become yellowish brown with a cheesy texture due to bacterial colonization and decay. HOST RANGE Potato is the main host of the pathogen, but natural infection also occurs on eggplant, tomato, and sugar beet. TAXONOMIC STATUS OF THE PATHOGEN Class: Actinobacteria; Order: Actinomycetales; Family: Microbacteriaceae; Genus: Clavibacter; Species: Clavibacter sepedonicus (Spieckermann and Kotthoff 1914) Li et al. 2018. SYNONYMS (NONPREFERRED SCIENTIFIC NAMES) Aplanobacter sepedonicus; Bacterium sepedonicum; Corynebacterium sepedonicum; Corynebacterium michiganense pv. sepedonicum; Clavibacter michiganensis subsp. sepedonicus. MICROBIOLOGICAL PROPERTIES Gram-positive, club-shaped cells with creamy to yellowish-cream colonies for which the optimal growth temperature is 20-23°C. DISTRIBUTION Asia (China, Japan, Kazakhstan, Nepal, North Korea, Pakistan, South Korea, Uzbekistan, the Asian part of Russia), Europe (Belarus, Bulgaria, Czech Republic, Estonia, Finland, Georgia, Germany, Greece, Hungary, Latvia, Lithuania, Norway, Poland, Romania, European part of Russia, Slovakia, Spain, Sweden, Turkey, Ukraine), and North America (Canada, Mexico, USA). PHYTOSANITARY CATEGORIZATION CORBSE: EPPO A2 list no. 51. EU; Annex designation I/A2.
Collapse
Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Jan M. van der Wolf
- Business Unit Biointeractions and Plant HealthWageningen University and ResearchWageningenNetherlands
| | - Hamid Abachi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Xiang Li
- Canadian Food Inspection Agency, Charlottetown LaboratoryCharlottetownPECanada
| | - Solke H. De Boer
- Canadian Food Inspection Agency, Charlottetown LaboratoryCharlottetownPECanada
| | | |
Collapse
|
7
|
Osdaghi E, Taghouti G, Dutrieux C, Taghavi SM, Fazliarab A, Briand M, Le Saux MF, Portier P, Jacques MA. Whole Genome Resources of 17 Curtobacterium flaccumfaciens Strains Including Pathotypes of C. flaccumfaciens pv. betae, C. flaccumfaciens pv. oortii, and C. flaccumfaciens pv. poinsettiae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:352-356. [PMID: 35021852 DOI: 10.1094/mpmi-11-21-0282-a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Geraldine Taghouti
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Cecile Dutrieux
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Amal Fazliarab
- Iranian Sugarcane Research and Training Institute (ISCRTI), Ahvaz, Khuzestan, Iran
| | - Martial Briand
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marion Fischer Le Saux
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Perrine Portier
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marie-Agnes Jacques
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| |
Collapse
|
8
|
Osdaghi E, Jones JB, Sharma A, Goss EM, Abrahamian P, Newberry EA, Potnis N, Carvalho R, Choudhary M, Paret ML, Timilsina S, Vallad GE. A centenary for bacterial spot of tomato and pepper. MOLECULAR PLANT PATHOLOGY 2021; 22:1500-1519. [PMID: 34472193 PMCID: PMC8578828 DOI: 10.1111/mpp.13125] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 05/08/2023]
Abstract
DISEASE SYMPTOMS Symptoms include water-soaked areas surrounded by chlorosis turning into necrotic spots on all aerial parts of plants. On tomato fruits, small, water-soaked, or slightly raised pale-green spots with greenish-white halos are formed, ultimately becoming dark brown and slightly sunken with a scabby or wart-like surface. HOST RANGE Main and economically important hosts include different types of tomatoes and peppers. Alternative solanaceous and nonsolanaceous hosts include Datura spp., Hyoscyamus spp., Lycium spp., Nicotiana rustica, Physalis spp., Solanum spp., Amaranthus lividus, Emilia fosbergii, Euphorbia heterophylla, Nicandra physaloides, Physalis pubescens, Sida glomerata, and Solanum americanum. TAXONOMIC STATUS OF THE PATHOGEN Domain, Bacteria; phylum, Proteobacteria; class, Gammaproteobacteria; order, Xanthomonadales; family, Xanthomonadaceae; genus, Xanthomonas; species, X. euvesicatoria, X. hortorum, X. vesicatoria. SYNONYMS (NONPREFERRED SCIENTIFIC NAMES) Bacterium exitiosum, Bacterium vesicatorium, Phytomonas exitiosa, Phytomonas vesicatoria, Pseudomonas exitiosa, Pseudomonas gardneri, Pseudomonas vesicatoria, Xanthomonas axonopodis pv. vesicatoria, Xanthomonas campestris pv. vesicatoria, Xanthomonas cynarae pv. gardneri, Xanthomonas gardneri, Xanthomonas perforans. MICROBIOLOGICAL PROPERTIES Colonies are gram-negative, oxidase-negative, and catalase-positive and have oxidative metabolism. Pale-yellow domed circular colonies of 1-2 mm in diameter grow on general culture media. DISTRIBUTION The bacteria are widespread in Africa, Brazil, Canada and the USA, Australia, eastern Europe, and south-east Asia. Occurrence in western Europe is restricted. PHYTOSANITARY CATEGORIZATION A2 no. 157, EU Annex designation II/A2. EPPO CODES XANTEU, XANTGA, XANTPF, XANTVE.
Collapse
Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Jeffrey B. Jones
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Anuj Sharma
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Erica M. Goss
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Peter Abrahamian
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
| | - Eric A. Newberry
- Department of Entomology and Plant PathologyAuburn UniversityAuburnAlabamaUSA
| | - Neha Potnis
- Department of Entomology and Plant PathologyAuburn UniversityAuburnAlabamaUSA
| | - Renato Carvalho
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Manoj Choudhary
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Mathews L. Paret
- Department of Plant PathologyNorth Florida Research and Education CenterUniversity of FloridaQuincyFloridaUSA
| | - Sujan Timilsina
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Gary E. Vallad
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
| |
Collapse
|
9
|
Chen G, Khojasteh M, Taheri-Dehkordi A, Taghavi SM, Rahimi T, Osdaghi E. Complete Genome Sequencing Provides Novel Insight Into the Virulence Repertories and Phylogenetic Position of Dry Beans Pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens. PHYTOPATHOLOGY 2021; 111:268-280. [PMID: 32716255 DOI: 10.1094/phyto-06-20-0243-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacterial wilt of dry beans (family Fabaceae) caused by the actinobacterial agent Curtobacterium flaccumfaciens pv. flaccumfaciens is one of the most important diseases threatening edible legume production around the globe. Despite the economic losses due to the bacterial wilt disease, the pathogen has not so far been investigated for its genomic features, pathogenicity determinants, and virulence strategies. Here we present the first complete genome sequence of a highly virulent bacteriocin-producing C. flaccumfaciens pv. flaccumfaciens strain P990. The bacterium has a circular chromosome consisting of 3,736 kbp with the G+C% content of 71.0%. Furthermore, a 147-kbp circular plasmid (pCff1) with 66.1% G+C% content as well as two circular plasmid-like DNAs with sizes of 25 and 22 kbp were detected within the genomic contents of C. flaccumfaciens pv. flaccumfaciens. Phylogenetic analyses revealed that only a few number of Curtobacterium sp. strains deposited in the public databases could be classified within the species C. flaccumfaciens. Comparative genomics of C. flaccumfaciens pv. flaccumfaciens using the genome sequences of actinobacterial plant pathogens revealed the presence of a set of unique low G+C% content genomic islands in the C. flaccumfaciens pv. flaccumfaciens genome. Homologs of pathogenicity-determinant loci capable of producing 1,4-beta-xylanase (xysA), pectate lyase (pelA1 and pelA2), serine protease (chpC, chpG, and pat-1), and sortase (srtA) were detected in C. flaccumfaciens pv. flaccumfaciens genome. The genomic data presented here extend our understanding of the C. flaccumfaciens pv. flaccumfaciens genomic features and pave the ways of research on functional and interaction genetics to combat the risk of bacterial wilt disease in the 21st century's dry bean industry.
Collapse
Affiliation(s)
- Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Moein Khojasteh
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ayat Taheri-Dehkordi
- Department of Horticultural Science, College of Agriculture & Natural Resources, University of Tehran, Karaj 31587-77871, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Touraj Rahimi
- Department of Agronomy and Plant Breeding, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| |
Collapse
|
10
|
Sedighian N, Taghavi SM, Hamzehzarghani H, van der Wolf JM, Wicker E, Osdaghi E. Potato-Infecting Ralstonia solanacearum Strains in Iran Expand Knowledge on the Global Diversity of Brown Rot Ecotype of the Pathogen. PHYTOPATHOLOGY 2020; 110:1647-1656. [PMID: 32401153 DOI: 10.1094/phyto-03-20-0072-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacterial wilt and brown rot disease caused by Ralstonia solanacearum species complex (RSSC) is one of the major constraints of potato (Solanum tuberosum) production around the globe. During 2017 to 2018, an extensive field survey was conducted in six potato-growing provinces of Iran to monitor the status of bacterial wilt disease. Pathogenicity and host range assays using 59 bacterial strains isolated in Iran showed that they were pathogenic on eggplant, red nightshade, pepper, potato and tomato, while nonpathogenic on common bean, cowpea, cucumber, sunflower, zinnia and zucchini. PCR-based diagnosis revealed that the strains belong to the phylotype IIB/sequevar 1 (IIB/I) lineage of the RSSC. Furthermore, a five-gene multilocus sequence analysis and typing (egl, fliC, gyrB, mutS, and rplB) confirmed the phylogenetically near-homogeneous nature of the strains within IIB/I lineage. Four sequence types were identified among 58 IIB/1 strains isolated in Iran. Phylogenetically near-homogeneous nature of the strains in Iran raise questions about the mode of inoculum entry of the bacterial wilt pathogen into the country (one-time introduction versus multiple introductions), while the geographic origin of the Iranian R. solanacearum strains remains undetermined. Furthermore, sequence typing showed that there were shared alleles (haplotypes) and sequence types among the strains isolated in geographically distant areas in Iran, suggesting intranational transmission of the pathogen in the country.
Collapse
Affiliation(s)
- Nasim Sedighian
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | | | - Jan M van der Wolf
- Wageningen University and Research, Business Unit Biointeractions and Plant Health, 6700 AA, Wageningen, The Netherlands
| | - Emmanuel Wicker
- IPME, Univ Montpellier, CIRAD, IRD, Montpellier, France
- CIRAD, UMR IPME, Montpellier, France
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| |
Collapse
|
11
|
Osdaghi E, Young AJ, Harveson RM. Bacterial wilt of dry beans caused by Curtobacterium flaccumfaciens pv. flaccumfaciens: A new threat from an old enemy. MOLECULAR PLANT PATHOLOGY 2020; 21:605-621. [PMID: 32097989 PMCID: PMC7170776 DOI: 10.1111/mpp.12926] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 05/20/2023]
Abstract
Bacterial wilt and tan spot of dry beans (family Fabaceae), caused by Curtobacterium flaccumfaciens pv. flaccumfaciens, is an important emerging disease threatening the edible legume industry around the globe. The management of bacterial wilt has been a major problem since its original description in 1922. This is in part due to the seedborne nature of the pathogen allowing the bacterium to be transmitted long distances via infected seeds, as well as a lack of detailed molecular information concerning the pathogenicity repertoires and virulence determinates of the pathogen. Identification can also be difficult owing to the presence of five different colony colour variants (i.e., yellow, orange, pink, purple, and red) on culture media. In this review, we provide an overview of the aetiology, epidemiology, and management strategies of bacterial wilt disease. First, a comprehensive and comparative symptomology of the disease on different dry bean species is described. Then, the taxonomic history of the causal agent and utility of high-throughput sequencing-based approaches in the precise characterization of the pathogen is explained. Furthermore, we provide an updated outline on the global distribution of the pathogen, highlighting expansion of the causal agent into the areas with no history of the disease until the beginning of the current century. Finally, because there are limited options for use of conventional pesticides against the pathogen, we highlight the use of integrated pest management strategies, for example quarantine inspections, resistant cultivars, and crop sanitation, to combat the risk of bacterial wilt disease in the dry bean industry. DISEASE SYMPTOMS Interveinal chlorosis on leaflets leading to necrotic areas and systemic wilt. Seed discolouration to yellow, orange, pink, or purple is seen in white-seeded cultivars. HOST RANGE Causes bacterial wilt and tan spot disease on edible dry beans in the Fabaceae family, including common bean (Phaseolus vulgaris), cowpea (Vigna unguiculata), mungbean (Vigna radiata), soybean (Glycine max), as well as a number of weed species. TAXONOMIC STATUS OF THE PATHOGEN Bacteria; phylum Actinobacteria; order Actinomycetales; suborder: Micrococcineae; family Microbacteriaceae; genus Curtobacterium; species Curtobacterium flaccumfaciens. SYNONYMS Corynebacterium flaccumfaciens subsp. flaccumfaciens; Corynebacterium flaccumfaciens pv. flaccumfaciens, Corynebacterium flaccumfaciens, Phytomonas flaccumfaciens, Bacterium flaccumfaciens. MICROBIOLOGICAL PROPERTIES Multicoloured (yellow, orange, pink, purple, and red), gram-positive, aerobic, curved rod, nonspore-forming, polar flagellated, motile cells. DISTRIBUTION Widespread in America (Brazil, Canada, and the USA), Australia, and Iran. Restricted occurrence in Africa and Europe. PHYTOSANITARY CATEGORIZATION EPPO A2 list no. 48, EU Annex II⁄B.
Collapse
Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureShiraz UniversityShirazIran
| | - Anthony J. Young
- School of Agriculture and Food SciencesThe University of QueenslandGattonQueenslandAustralia
| | - Robert M. Harveson
- University of NebraskaPanhandle Research & Extension CenterScottsbluffUSA
| |
Collapse
|
12
|
Hamidizade M, Taghavi SM, Martins SJ, Herschlag RA, Hockett KL, Bull CT, Osdaghi E. Bacterial Brown Pit, a New Disease of Edible Mushrooms Caused by Mycetocola sp. PLANT DISEASE 2020; 104:1445-1454. [PMID: 32181723 DOI: 10.1094/pdis-10-19-2176-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
From September to December 2018, commercial button mushroom (Agaricus bisporus) farms in central Iran were surveyed to monitor the causal agent(s) of browning and blotch symptoms on mushroom caps. In addition to dozens of pseudomonads (i.e., Pseudomonas tolaasii and Pseudomonas reactans), six slow-growing gram-positive bacterial strains were isolated from blotched mushroom caps. These bacteria presented as creamy white, circular, smooth, nonfluorescent, and shiny colonies with whole margins resembling members of Microbacteriaceae (Actinobacteria). All of the actinobacterial strains were aggressively pathogenic on cut cap surface of two edible mushrooms (i.e., A. bisporus and Pleurotus eryngii), inducing brown pit symptoms 48 h postinoculation. The strains did not induce symptoms on the vegetables tested (i.e., carrot, cucumber, and potato), and they did not affect the growth of mycelium of tested plant-pathogenic fungi (i.e., Acremonium sp., Fusarium spp., and Phytopythium sp.). Phylogeny of 16S ribosomal RNA and multilocus sequence analysis of six housekeeping genes (i.e., atpD, dnaK, gyrB, ppK, recA, and rpoB) revealed that the bacterial strains belong to the actinobacterial genus Mycetocola spp., whereas the species status of the strains remains undetermined. Mushroom-associated Mycetocola species were previously reported to be capable of detoxifying tolaasin, a toxin produced by P. tolaasii, whereas the strains isolated in this study did not show tolaasin detoxification activities. Altogether, this is the first report of a mushroom disease caused by an actinobacterial species, and "bacterial brown pit" was assigned as the common name of the disease.
Collapse
Affiliation(s)
- Mozhde Hamidizade
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Samuel J Martins
- Plant Pathology & Environmental Microbiology Department, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Rachel A Herschlag
- Plant Pathology & Environmental Microbiology Department, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Kevin L Hockett
- Plant Pathology & Environmental Microbiology Department, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Carolee T Bull
- Plant Pathology & Environmental Microbiology Department, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| |
Collapse
|
13
|
Comparative Genomics and Phylogenetic Analyses Suggest Several Novel Species within the Genus Clavibacter, Including Nonpathogenic Tomato-Associated Strains. Appl Environ Microbiol 2020; 86:AEM.02873-19. [PMID: 31924620 DOI: 10.1128/aem.02873-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Members of the genus Clavibacter are economically important bacterial plant pathogens infecting a set of diverse agricultural crops (e.g., alfalfa, corn, potato, tomato, and wheat). Tomato-associated Clavibacter sp. strains account for a great portion of the genetic diversity of the genus, and C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis), causing bacterial canker disease, is considered one of the most destructive seed-borne agents for the crop worldwide. However, current taxonomic descriptions of the genus do not reflect the existing diversity of the strains, resulting in unsatisfactory results in quarantine surveys for the pathogens. In this study, we used all the available genome sequences of Clavibacter sp. strains, including the type strains of newly described subspecies, to provide precise insight into the diversity of tomato-associated members of the genus and further clarify the taxonomic status of the strains using genotypic and phenotypic features. The results of phylogenetic analyses revealed the existence of nine hypothetical new species among the investigated strains. None of the three new subspecies (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) is included within the tomato-pathogenic C. michiganensis sensu stricto lineage. Although comparative genomics revealed the lack of chp and tomA pathogenicity determinant gene clusters in the nonpathogenic strains, a number of pathogenicity-related genes were noted to be present in all the strains regardless of their pathogenicity characteristics. Altogether, our results indicate a need for a formal taxonomic reconsideration of tomato-associated Clavibacter sp. strains to facilitate differentiation of the lineages in quarantine inspections.IMPORTANCE Clavibacter spp. are economically important bacterial plant pathogens infecting a set of diverse agricultural crops, such as alfalfa, corn, pepper, potato, tomato, and wheat. A number of plant-pathogenic members of the genus (e.g., C. michiganensis sensu stricto and C. sepedonicus, infecting tomato and potato plants, respectively) are included in the A2 (high-risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Although tomato-associated members of Clavibacter spp. account for a significant portion of the genetic diversity in the genus, only the strains belonging to C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis) cause bacterial canker disease of tomato and are subjected to the quarantine inspections. Hence, discrimination between the pathogenic and nonpathogenic Clavibacter sp. strains associated with tomato seeds and transplants plays a pivotal role in the accurate detection and cost-efficient management of the disease. On the other hand, detailed information on the genetic contents of different lineages of the genus would lead to the development of genome-informed specific detection techniques. In this study, we have provided an overview of the phylogenetic and genomic differences between the pathogenic and nonpathogenic tomato-associated Clavibacter sp. strains. We also noted that the taxonomic status of newly introduced subspecies of C. michiganensis (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) should be reconsidered.
Collapse
|