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Urzo MLR, Guinto TD, Eusebio-Cope A, Budot BO, Yanoria MJT, Jonson GB, Arakawa M, Kondo H, Suzuki N. Metatranscriptomic Sequencing of Sheath Blight-Associated Isolates of Rhizoctonia solani Revealed Multi-Infection by Diverse Groups of RNA Viruses. Viruses 2024; 16:1152. [PMID: 39066314 PMCID: PMC11281561 DOI: 10.3390/v16071152] [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: 06/14/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Rice sheath blight, caused by the soil-borne fungus Rhizoctonia solani (teleomorph: Thanatephorus cucumeris, Basidiomycota), is one of the most devastating phytopathogenic fungal diseases and causes yield loss. Here, we report on a very high prevalence (100%) of potential virus-associated double-stranded RNA (dsRNA) elements for a collection of 39 fungal strains of R. solani from the rice sheath blight samples from at least four major rice-growing areas in the Philippines and a reference isolate from the International Rice Research Institute, showing different colony phenotypes. Their dsRNA profiles suggested the presence of multiple viral infections among these Philippine R. solani populations. Using next-generation sequencing, the viral sequences of the three representative R. solani strains (Ilo-Rs-6, Tar-Rs-3, and Tar-Rs-5) from different rice-growing areas revealed the presence of at least 36 viruses or virus-like agents, with the Tar-Rs-3 strain harboring the largest number of viruses (at least 20 in total). These mycoviruses or their candidates are believed to have single-stranded RNA or dsRNA genomes and they belong to or are associated with the orders Martellivirales, Hepelivirales, Durnavirales, Cryppavirales, Ourlivirales, and Ghabrivirales based on their coding-complete RNA-dependent RNA polymerase sequences. The complete genome sequences of two novel RNA viruses belonging to the proposed family Phlegiviridae and family Mitoviridae were determined.
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Affiliation(s)
- Michael Louie R. Urzo
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines; (M.L.R.U.); (T.D.G.)
| | - Timothy D. Guinto
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines; (M.L.R.U.); (T.D.G.)
| | - Ana Eusebio-Cope
- Fit-for-Future Genetic Resources Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
| | - Bernard O. Budot
- Institute of Weed Science, Entomology, and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines;
| | - Mary Jeanie T. Yanoria
- Traits for Challenged Environments Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines; (M.J.T.Y.); (G.B.J.)
| | - Gilda B. Jonson
- Traits for Challenged Environments Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines; (M.J.T.Y.); (G.B.J.)
| | - Masao Arakawa
- Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan;
| | - Hideki Kondo
- Plant-Microbe Interactions Group, Institute of Plant Science and Resources (IPSR), Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan
| | - Nobuhiro Suzuki
- Plant-Microbe Interactions Group, Institute of Plant Science and Resources (IPSR), Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan
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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. THE NEW PHYTOLOGIST 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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