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Al-Mahmooli IH, Finckh MR, Velazhahan R, AlJabri AM, Šišić A, Hussain S, Abdel-Jalil R, Al-Sadi AM. Pythium and Globisporangium species associated with cucumber rhizosphere causing damping-off and their effects on cucumber seed decay in Oman. Arch Microbiol 2024; 206:374. [PMID: 39127775 DOI: 10.1007/s00203-024-04097-y] [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: 03/11/2024] [Revised: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
Pythium sensu lato (s.l.) is a pathogenic oomycete. The present study was conducted to isolate and identify Pythium s.l. species associated with the rhizosphere and roots of greenhouse-growing cucumbers showing damping-off symptoms in 10 Omani governorates (provinces). A total of 166 isolates were recovered from 276 rhizosphere soil and root samples and were identified based on the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region and the cytochrome c oxidase subunit I (COX I) gene region. Pythium aphanidermatum, P. myriotylum, Globisporangium spinosum, Globisporangium sp.1 (isolates Kb003/PySyCu-1 and Kb004/PySyCu-2), and Globisporangium sp.2 (isolate Ib002R) were identified. Among these species, P. aphanidermatum was the most abundant species, represented by 143 isolates (86.1%), followed by G. spinosum with 18 isolates (10.8%), Globisporangium sp.1 and P. myriotylum each with 2 isolates (2.4%), and Globisporangium sp.2 with 1 isolate (0.6%). Pathogenicity tests were also conducted for 38 isolates, including P. aphanidermatum (25), P. myriotylum (2), Globisporangium sp.2 (1), G. spinosum (8), and Globisporangium sp.1 (2). Among the tested isolates, only Globisporangium sp.2 isolate was avirulent, and none of the seeds were rotted at the end of the treatment. However, the other species induced the symptoms of seed decay with the incidence ranged from 86.7 to 100%. Phylogenetic analyses were conducted based on 222 ITS and 53 COX I sequences, and confirmed morphological identification. In addition, the genetic diversity of 93 P. aphanidermatum isolates was assessed via the amplified fragment length polymorphism (AFLP) method. The analysis produced 93 genotypes and 449 polymorphic loci. Pythium aphanidermatum populations were found to have moderate levels of genetic diversity (H = 0.2) and a moderate Shannon information index (I = 0.3793). Analysis of molecular variance (FST = 0.1, P = 0.0) revealed a moderate level of genetic differentiation among P. aphanidermatum isolates between Oman governorates. The sensitivity of 15 P. aphanidermatum isolates was evaluated against hymexazol at different concentrations (10, 100, and 1000 ppm). The results revealed that P. aphanidermatum could grow well at concentrations of up to 100 ppm hymexazol. However, hymexazol at 1000 ppm retarded the growth of P. aphanidermatum. This study showed that P. aphanidermatum is the most prevalent species in greenhouses in Oman and exhibited a moderate level of genetic diversity. Most of the isolates exhibited differences in tolerance to hymexazol but showed no resistance.
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Affiliation(s)
- Issa Hashil Al-Mahmooli
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Muscat, 123, Oman.
- Faculty Organic Agricultural Sciences, Kassel University, Fachbereich 11-Fachgebiet Ökologischer Pflanzenschutz Nordbahnhofstraße1a, 37213, Witzenhausen, Germany.
| | - Maria Renate Finckh
- Faculty Organic Agricultural Sciences, Kassel University, Fachbereich 11-Fachgebiet Ökologischer Pflanzenschutz Nordbahnhofstraße1a, 37213, Witzenhausen, Germany
| | - Rethinasamy Velazhahan
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Muscat, 123, Oman
| | - AlMohanad Mohammed AlJabri
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Muscat, 123, Oman
| | - Adnan Šišić
- Faculty Organic Agricultural Sciences, Kassel University, Fachbereich 11-Fachgebiet Ökologischer Pflanzenschutz Nordbahnhofstraße1a, 37213, Witzenhausen, Germany
| | - Shah Hussain
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Muscat, 123, Oman
| | - Raid Abdel-Jalil
- Department of Chemistry, College of Science, Sultan Qaboos University, Al-Khod, Muscat, 123, Oman
| | - Abdullah Mohammed Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Muscat, 123, Oman
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Salmaninezhad F, Mostowfizadeh-Ghalamfarsa R, Cacciola SO. Pythium banihashemianum sp. nov. and Globisporangium izadpanahii sp. nov.: Two New Oomycete Species from Rice Paddies in Iran. J Fungi (Basel) 2024; 10:405. [PMID: 38921391 PMCID: PMC11204656 DOI: 10.3390/jof10060405] [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: 03/25/2024] [Revised: 05/31/2024] [Accepted: 06/02/2024] [Indexed: 06/27/2024] Open
Abstract
An investigation into oomycete diversity in rice paddies of Fars Province in Iran led to the identification of two new Pythium sensu lato (s.l.) species as Globisporangium izadpanahii sp. nov. and Pythium banihashemianum sp. nov. The identification was based on morphological and physiological features as well as on the phylogenetic analysis of nuclear (ITS and βtub) and mitochondrial (cox1 and cox2) loci using Bayesian inference and Maximum Likelihood. The present paper formally describes these two new species and defines their phylogenetic relationships with other congeneric species. According to multiple gene genealogy analysis, G. izadpanahii sp. nov. was grouped with other species of Globisporangium (formerly, clade G of Pythium s.l.) and was closely related to both G. nagaii and the recently described G. coniferarum. The second species, designated P. banihashemianum sp. nov., was grouped with other species of Pythium sensu stricto (formerly, clade B of Pythium s.l.) and, according to the phylogenetic analysis, shared an ancestor with P. plurisporium. The production of globose hyphal swellings was a major characteristic of G. izadpanahii sp. nov., which did not produce vesicles and zoospores. In pathogenicity tests on rice seedlings, P. banihashemianum sp. nov. isolates were highly pathogenic and caused severe root and crown rot, while G. izadpanahii sp. nov. isolates were not pathogenic.
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Affiliation(s)
- Fatemeh Salmaninezhad
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 7144167186, Iran;
| | | | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy
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Nguyen HDT, Dodge A, Dadej K, Rintoul TL, Ponomareva E, Martin FN, de Cock AWAM, Lévesque CA, Redhead SA, Spies CFJ. Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium. Mycologia 2022; 114:501-515. [PMID: 35522547 DOI: 10.1080/00275514.2022.2045116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1-D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of Pythium s.l. The status of alternative generic names that have been used for species of Pythium in the past (e.g., Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium) was investigated. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.
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Affiliation(s)
- Hai D T Nguyen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Annette Dodge
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Kasia Dadej
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Tara L Rintoul
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Ekaterina Ponomareva
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Frank N Martin
- Crop Improvement and Protection Research, Agricultural Research Service, United States Department of Agriculture, Salinas, California 93905, USA
| | - Arthur W A M de Cock
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - C André Lévesque
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Scott A Redhead
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Christoffel F J Spies
- Plant Microbiology, Agricultural Research Council - Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
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Li M, Hieno A, Motohashi K, Suga H, Kageyama K. Pythium intermedium, a species complex consisting of three phylogenetic species found in cool-temperate forest ecosystems. Fungal Biol 2021; 125:1017-1025. [PMID: 34776229 DOI: 10.1016/j.funbio.2021.07.004] [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: 04/19/2020] [Revised: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Pythium intermedium plays a vital role in the carbon cycle of cool-temperate forests and is widely distributed in Japan's forest soils. In this study, we performed a phylogenetic analysis of the P. intermedium species complex using DNA sequences from multiple loci. The study included 35 isolates from cool-temperate forest soils, seven known P. intermedium isolates, and six known Pythium attrantheridium isolates. We also performed morphological observations and mating tests. Our results showed that all the isolates formed one large clade but were divided into three subclades. Furthermore, we observed many mating reactions between isolates from different subclades, including between P. attrantheridium and P. intermedium. Therefore, we suggest that P. intermedium, P. attrantheridium, and another phylogenetic species belong to one species complex. This is the first report of a species complex within P. intermedium and will be helpful in understanding the evolution of Pythium species in natural ecosystems.
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Affiliation(s)
- Mingzhu Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China; River Basin Research Center, Gifu University, Gifu, 501-1193, Japan.
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Keiichi Motohashi
- Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
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Jayawardena RS, Hyde KD, Chen YJ, Papp V, Palla B, Papp D, Bhunjun CS, Hurdeal VG, Senwanna C, Manawasinghe IS, Harischandra DL, Gautam AK, Avasthi S, Chuankid B, Goonasekara ID, Hongsanan S, Zeng X, Liyanage KK, Liu N, Karunarathna A, Hapuarachchi KK, Luangharn T, Raspé O, Brahmanage R, Doilom M, Lee HB, Mei L, Jeewon R, Huanraluek N, Chaiwan N, Stadler M, Wang Y. One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020). FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00460-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThis is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.
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