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Boie W, Schemmel M, Ye W, Hasler M, Goll M, Verreet JA, Cai D. An assessment of the species diversity and disease potential of Pythium communities in Europe. Nat Commun 2024; 15:8369. [PMID: 39333145 PMCID: PMC11437173 DOI: 10.1038/s41467-024-52761-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/19/2024] [Indexed: 09/29/2024] Open
Abstract
Pythium sensu lato (s.l.) is a genus of parasitic oomycetes that poses a serious threat to agricultural production worldwide, but their severity is often neglected because little knowledge about them is available. Using an internal transcribed spacer (ITS) amplicon-based-metagenomics approach, we investigate the occurrence, abundance, and diversity of Pythium spp. s.l. in 127 corn fields of 11 European countries from the years 2019 to 2021. We also identify 73 species, with up to 20 species in a single soil sample, and the prevalent species, which show high species diversity, varying disease potential, and are widespread in most countries. Further, we show species-species co-occurrence patterns considering all detected species and link species abundance to soil parameter using the LUCAS topsoil dataset. Infection experiments with recovered isolates show that Pythium s.l. differ in disease potential, and that effective interference with plant hormone networks suppressing JA (jasmonate)-mediated defenses is an essential component of the virulence mechanism of Pythium s.l. species. This study provides a valuable dataset that enables deep insights into the structure and species diversity of Pythium s.l. communities in European corn fields and knowledge for better understanding plant-Pythium interactions, facilitating the development of an effective strategy to cope with this pathogen.
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Affiliation(s)
- Wilken Boie
- Molecular Phytopathology and Biotechnology, Institute for Phytopathology, Christian-Albrechts-University of Kiel, Hermann-Rodewald Str. 9, Kiel, Germany
| | - Markus Schemmel
- Molecular Phytopathology and Biotechnology, Institute for Phytopathology, Christian-Albrechts-University of Kiel, Hermann-Rodewald Str. 9, Kiel, Germany
| | - Wanzhi Ye
- Molecular Phytopathology and Biotechnology, Institute for Phytopathology, Christian-Albrechts-University of Kiel, Hermann-Rodewald Str. 9, Kiel, Germany
| | - Mario Hasler
- Lehrfach Variationsstatistik, Christian-Albrechts-University of Kiel, Hermann-Rodewald Str. 9, Kiel, Germany
| | - Melanie Goll
- Syngenta Agro GmbH, Lindleystraße 8 D, Frankfurt am Main, Germany
| | - Joseph-Alexander Verreet
- Phytopathology and Crop Protection, Institute for Phytopathology, Christian-Albrechts-University of Kiel, Hermann-Rodewald Str. 9, Kiel, Germany
| | - Daguang Cai
- Molecular Phytopathology and Biotechnology, Institute for Phytopathology, Christian-Albrechts-University of Kiel, Hermann-Rodewald Str. 9, Kiel, Germany.
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Syu ZJ, Tu CK, Chen CY, Lo SF, Lee MH. A Large-Scale Hydroponic Evaluation of Rice Mutants for Pythium Resistance. PLANT DISEASE 2024; 108:2309-2320. [PMID: 38054926 DOI: 10.1094/pdis-10-23-2179-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Rice is a major staple crop worldwide. However, the occurrence of rice diseases during cultivation poses a significant challenge to achieving optimal yields. Among the major pathogens, Pythium species, which cause seedling blight, are of particular concern. Pythium infects rice roots through zoospores, mycelia, or oospores, leading to root rot, stunting, yellowing, and ultimately seedling damping-off. While many disease resistance-related genes have been reported in rice, only very limited research has been associated with resistance to Pythium infection. In this study, we aimed to establish a rapid screening system to identify rice lines that are resistant or susceptible to the Pythium pathogen in rice nurseries. We conducted evaluations on important factors, including virulence, inoculation method, seed-soaking period, and the measurement of disease severity. As a result, we successfully developed a screening system that allows for high-throughput and rapid screening of the Taiwan Rice Insertional Mutant (TRIM) library for mutant lines exhibiting resistance to P. arrhenomanes. Furthermore, we identified a slightly resistant TRIM line and explored potential genes encoding endoglucanase-1 precursor and malonyl-CoA decarboxylase that may be involved in conferring resistance to P. arrhenomanes.
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Affiliation(s)
- Zun-Jie Syu
- Department of Plant Pathology, National Chung Hsing University, Taichung 40277, Taiwan
| | - Chi-Kuan Tu
- Department of Plant Pathology, National Chung Hsing University, Taichung 40277, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 40277, Taiwan
| | - Chi-Yu Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung 40277, Taiwan
| | - Shuen-Fang Lo
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 40277, Taiwan
- International Doctoral Program in Agribusiness, National Chung Hsing University, Taichung 40277, Taiwan
| | - Miin-Huey Lee
- Department of Plant Pathology, National Chung Hsing University, Taichung 40277, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 40277, Taiwan
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3
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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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4
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Li Y, Yang R, Guo L, Gao W, Su P, Xu Z, Xiao H, Ma Z, Liu X, Gao P, Li B, Sun X, Yan G, Sun W. The composition, biotic network, and assembly of plastisphere protistan taxonomic and functional communities in plastic-mulching croplands. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128390. [PMID: 35152106 DOI: 10.1016/j.jhazmat.2022.128390] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
The increasing use of plastic film mulching has caused the accumulation of plastic film residue in soil. To date, most researches on the plastisphere have focused on bacterial and fungal communities, with few on protistan community, especially in terrestrial ecosystems. To understand plastisphere protistan communities, we collected plastic film residues from plastic-mulching croplands. The plastisphere significantly altered the alpha-diversity, structure, and composition of taxonomic and functional (consumers, phototrophs, and parasites) communities. In both the plastisphere and surrounding soil, although some consumers dominated the protistan community network, while their performance was weakened by mulch application. The ecological networks of the plastisphere community presented higher modularity, less complexity, and a lower proportion of positive connections than the networks of surrounding soil. In addition, the enriched plant pathogens (e.g., Spongospora) and keystone taxa classified as plant pathogens (e.g., Pythium) in the plastisphere imply that plastic film residues may pose a risk to soil health and plant performance. Neutral-based processes dominated the assembly of the plastisphere protistan communities, whereas niche-based processes governed the protistan community assembly of surrounding soil. This study reveals that plastic film residues generate a unique niche for protistan colonization, which disturbs protistan communities and threatens agricultural ecosystem health and function.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Rui Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Lifang Guo
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Wenlong Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Pingzhou Su
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Zhimin Xu
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Huan Xiao
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zhixiong Ma
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xiang Liu
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Geng Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China.
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Kamali-Sarvestani S, Mostowfizadeh-Ghalamfarsa R, Salmaninezhad F, Cacciola SO. Fusarium and Neocosmospora Species Associated with Rot of Cactaceae and Other Succulent Plants. J Fungi (Basel) 2022; 8:364. [PMID: 35448595 PMCID: PMC9024871 DOI: 10.3390/jof8040364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/21/2022] [Accepted: 03/26/2022] [Indexed: 01/31/2023] Open
Abstract
Infections by Fusarium and Fusarium-like species on cacti and other succulent plants cause the syndrome known as Fusarium dry rot and soft rot. There are only few records of Fusarium species as pathogens of cacti and other succulent plants from Iran. The objective of this study was the identification and characterization of fusarioid species recovered from ornamental succulents in Shiraz County, Iran. Three fusarioid species, including F. oxysporum, F. proliferatum, and Neocosmospora falciformis (formerly F. falciforme), were recovered from 29 diverse species of cacti and other succulents with symptoms of Fusarium dry rot and soft rot. The three fungal species were identified on the basis of morphological characters and the phylogenetic analysis of the translation elongation factor1-α (tef1) nuclear gene. The F. oxysporum isolates were identified as F. oxysporum f. sp. opuntiarum. The pathogenicity of the three fusarioid species was tested on a range of economically important ornamental succulents, mostly in the Cactaceae family. The three species showed a broad host spectrum and induced different types of symptoms on inoculated plants, including soft and dry rot, chlorosis, necrotic spots, wilt, drying, root and crown rot. This is the first report of N. falciformis as a pathogen of succulent plants worldwide.
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Affiliation(s)
- Sahar Kamali-Sarvestani
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.K.-S.); (F.S.)
| | | | - Fatemeh Salmaninezhad
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.K.-S.); (F.S.)
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy
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6
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Doni F, Suhaimi NSM, Mispan MS, Fathurrahman F, Marzuki BM, Kusmoro J, Uphoff N. Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of 'Omics' Technologies. Int J Mol Sci 2022; 23:737. [PMID: 35054923 PMCID: PMC8775878 DOI: 10.3390/ijms23020737] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/03/2022] [Accepted: 01/08/2022] [Indexed: 12/26/2022] Open
Abstract
Rice, the main staple food for about half of the world's population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial-rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.
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Affiliation(s)
- Febri Doni
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia; (B.M.M.); (J.K.)
| | - Nurul Shamsinah Mohd Suhaimi
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (N.S.M.S.); (M.S.M.)
| | - Muhamad Shakirin Mispan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (N.S.M.S.); (M.S.M.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur 50603, Malaysia
| | - F Fathurrahman
- Department of Agrotechnology, Faculty of Agriculture, Universitas Islam Riau, Pekanbaru 28284, Indonesia;
| | - Betty Mayawatie Marzuki
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia; (B.M.M.); (J.K.)
| | - Joko Kusmoro
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia; (B.M.M.); (J.K.)
| | - Norman Uphoff
- SRI International Network and Resources Center, Cornell University, Ithaca, NY 14853, USA;
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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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