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Ujimatsu R, Takino J, Aoki S, Nakamura M, Haba H, Minami A, Hiruma K. A fungal transcription factor converts a beneficial root endophyte into an anthracnose leaf pathogen. Curr Biol 2025; 35:1989-2005.e6. [PMID: 40215963 DOI: 10.1016/j.cub.2025.03.026] [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: 09/27/2024] [Revised: 02/26/2025] [Accepted: 03/13/2025] [Indexed: 05/08/2025]
Abstract
Plant-associated fungi exhibit diverse lifestyles. Fungal endophytes are resident inside plant tissue without showing any disease symptoms for at least a part of their life cycle, and some of them benefit plant growth and health. However, some can cause diseases in specific host environments or genotypes, implying a virulence mechanism, which may be induced by as-yet-unidentified regulatory factors in fungal endophytes. Here, we show that CtBOT6, a transcription factor encoded within a secondary metabolite gene cluster known as the abscisic acid (ABA)-botrydial gene (ABA-BOT) cluster in the root-associated fungus Colletotrichum tofieldiae, triggers virulence-related gene expression and drives the production of diverse metabolites encoded both within and outside the cluster. CtBOT6 overexpression is sufficient to shift a root-beneficial C. tofieldiae to a leaf pathogen, driving its transition along the mutualist-pathogen continuum. Our genetic analysis revealed that the ABA-BOT cluster is indispensable for fungal virulence caused by CtBOT6 activation, implying that compounds derived from the cluster affect these processes. Furthermore, transcriptome analysis of root colonization by C.tofieldiae strains overexpressing CtBOT6 revealed that the pathogenic state induced plant defense and senescence responses characteristic of necrotrophic interactions. Importantly, this state enabled the fungus to proliferate and reproduce in leaves, in addition to heavily colonizing roots, with these processes being partly dependent on the host ABA and ethylene pathways. Our findings indicate that the expression status of CtBOT6 serves as a critical determinant for the endophytic fungus to adapt to the different plant tissues and to manifest diverse infection strategies.
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Affiliation(s)
- Ren Ujimatsu
- Department of Life Sciences, Multidisciplinary Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Junya Takino
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Seishiro Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-0882, Japan
| | - Masami Nakamura
- Department of Life Sciences, Multidisciplinary Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hiromi Haba
- Department of Life Sciences, Multidisciplinary Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Atsushi Minami
- Department of Chemistry, Institute of Science Tokyo, Tokyo 152-8551, Japan
| | - Kei Hiruma
- Department of Life Sciences, Multidisciplinary Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo (CRIIM, UTokyo), Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
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Zuccaro A, Di Pietro A. Plant-microbe interactions: A transcriptional switch governing fungal lifestyle shifts. Curr Biol 2025; 35:R353-R355. [PMID: 40328225 DOI: 10.1016/j.cub.2025.03.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2025]
Abstract
Fungi interact with plants in ways that can be beneficial or detrimental. A new study demonstrates that upregulating a single transcription factor in a beneficial fungal endophyte is sufficient to convert it into a pathogen.
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Affiliation(s)
- Alga Zuccaro
- Institute for Plant Sciences, University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), 50674 Cologne, Germany.
| | - Antonio Di Pietro
- Departamento de Genética, Universidad de Córdoba, 14014 Córdoba, Spain.
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3
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Dos Reis JBA, Steindorff AS, Lorenzi AS, Pinho DB, do Vale HMM, Pappas GJ. How genomics can help unravel the evolution of endophytic fungi. World J Microbiol Biotechnol 2025; 41:153. [PMID: 40289066 DOI: 10.1007/s11274-025-04375-x] [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: 03/10/2025] [Accepted: 04/18/2025] [Indexed: 04/29/2025]
Abstract
Endophytic fungi (EFs) form intimate associations with plants, residing within their tissues without causing apparent harm. Understanding the evolution of endophytic fungal genomes is essential for uncovering the mechanisms that drive their symbiotic relationships with host plants. This review explores the dynamic interactions between EFs and host plants, focusing on the evolutionary processes that shape their genomes. We highlighted key genomic adaptations promoting their endophytic lifestyle, including genes involved in plant cell wall degradation, secondary metabolite production, and stress tolerance. By combining genomic data with ecological and physiological information, this review provides a comprehensive understanding of the coevolutionary dynamics between EFs and host plants. Moreover, it provides insights that help elucidate the complex interdependencies governing their symbiotic interactions.
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Affiliation(s)
| | | | - Adriana Sturion Lorenzi
- Department of Cellular Biology, University of Brasília (UnB), Institute of Biological Sciences, Brasília, DF, Brazil
- Science of Beer Research Group, Science of Beer Institute, Florianópolis, SC, Brazil
| | - Danilo Batista Pinho
- Department of Phytopathology, University of Brasília (UnB), Institute of Biological Sciences, Brasília, DF, Brazil
| | - Helson Mario Martins do Vale
- Department of Phytopathology, University of Brasília (UnB), Institute of Biological Sciences, Brasília, DF, Brazil
| | - Georgios Joannis Pappas
- Department of Cellular Biology, University of Brasília (UnB), Institute of Biological Sciences, Brasília, DF, Brazil
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4
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Shi H, Sun B, Sun B, Wang X, Li B, Wu F, Tian T. Bacillus velezensis TB918 mitigates garlic dry rot disease by forming consortia with Pseudomonas in the rhizosphere and bulb. Front Microbiol 2025; 16:1567108. [PMID: 40303477 PMCID: PMC12037484 DOI: 10.3389/fmicb.2025.1567108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2025] [Accepted: 04/01/2025] [Indexed: 05/02/2025] Open
Abstract
Garlic dry rot (GDR), primarily caused by Fusarium proliferatum, is a significant postharvest disease that leads to substantial economic losses. Our previous research demonstrated that supplementing Bacillus-based biocontrol formulations with sucrose could boost its efficiency in protecting plants by building a hostile rhizomicrobiome for destructive soil-borne pathogens. B. velezensis TB918, previously isolated from pepper rhizosphere soil, exhibited a strong in vitro antifungal effect on Fusarium. In this study, we conducted a field experiment to investigate the efficacy of B. velezensis TB918 in controlling GDR, and explored the changes in microbial communities in garlic plants and rhizosphere soil following the application of TB918 with or without sucrose supplementation. Using 16S rRNA and ITS amplicon sequencing, we found that the introduction of TB918 significantly increased the abundance of Pseudomonas in garlic rhizosphere, especially when combined with sucrose. Three Pseudomonas strains were isolated from garlic tissues and rhizosphere soil treated with TB918 and sucrose, among which the GP2 strain exhibited antagonistic effects against pathogen ad planta. Co-culture and colonization assays showed that TB918 facilitated the biofilm formation of Pseudomonas strain by forming consortia. Interestingly, the abundance of potentially non-pathogenic Fusarium concentricum also increased, suggesting a potential niche exclusion effect. Our results demonstrated that TB918 in combination with sucrose effectively reduced the incidence of GDR during storage. This study provides valuable insights into the use of biocontrol agents and sucrose to modulate the garlic microbial community and suppress soil-borne pathogens.
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Affiliation(s)
- Haowen Shi
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Bingbing Sun
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Beiying Sun
- Department of Geography, University College London, London, United Kingdom
| | - Xiuli Wang
- Lanzhou Productivity Promoting Center, Gansu, China
| | - Bing Li
- Tianjin Agricultural Development Service Center, Tianjin, China
| | - Feng Wu
- Institute of Vegetables, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Tao Tian
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, China
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Yang N, Shan X, Wang K, Lu J, Zhu Y, Regina RS, Rodriguez RJ, Yao J, Martin FM, Yuan Z. A fusarioid fungus forms mutualistic interactions with poplar trees that resemble ectomycorrhizal symbiosis. IMA Fungus 2025; 16:e143240. [PMID: 40093759 PMCID: PMC11909594 DOI: 10.3897/imafungus.16.143240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Accepted: 01/28/2025] [Indexed: 03/19/2025] Open
Abstract
Fusarium species, recognised as global priority pathogens, frequently induce severe diseases in crops; however, certain species exhibit alternative symbiotic lifestyles and are either non-pathogenic or endophytic. In this study, we characterised the mutualistic relationship between the eFp isolate of F.pseudograminearum and five poplar species, resulting in formation root structures reminiscent of ectomycorrhizal (ECM) symbiosis. This functional symbiosis is evidenced by enhanced plant growth, reciprocal nutrient exchange, improved nitrogen and phosphorus uptake and upregulation of root sugar transporter gene expression (PtSweet1). Comparative and population genomics confirmed that eFp maintains a structurally similar genome, but exhibits significant divergence from ten conspecific pathogenic isolates. Notably, eFp enhanced the growth of diverse plant lineages (Oryza, Arabidopsis, Pinus and non-vascular liverworts), indicating a near-complete loss of virulence. Although this specialised symbiosis has only been established in vitro, it holds significant value in elucidating the evolutionary track from endophytic to mycorrhizal associations.
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Affiliation(s)
- Ningning Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China Research Institute of Subtropical Forestry, Chinese Academy of Forestry Hangzhou China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry Beijing China
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Hangzhou 311400, China Zhejiang Key Laboratory of Forest Genetics and Breeding Hangzhou China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China Nanjing Forestry University Nanjing China
| | - Xiaoliang Shan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China Nanjing Forestry University Nanjing China
- College of Plant Protection, Nanjing Agricultural University, Nanjing 21004, China Nanjing Agricultural University Nanjing China
| | - Kexuan Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China Nanjing Forestry University Nanjing China
| | - Junkun Lu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China Research Institute of Subtropical Forestry, Chinese Academy of Forestry Hangzhou China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China Research Institute of Tropical Forestry, Chinese Academy of Forestry Guangzhou China
| | - Ying Zhu
- Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, China Institute of Biology, Gansu Academy of Sciences Lanzhou China
| | - Redman S Regina
- Adaptive Symbiotic Technologies, University of Washington, Seattle, WA 98195, USA University of Washington Seattle United States of America
| | - Russell J Rodriguez
- Adaptive Symbiotic Technologies, University of Washington, Seattle, WA 98195, USA University of Washington Seattle United States of America
| | - Jiajia Yao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China Nanjing Forestry University Nanjing China
| | - Francis M Martin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China Nanjing Forestry University Nanjing China
- INRA, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, Champenoux, France INRA-Université de Lorraine 'Interactions Arbres/Microorganismes' Champenoux France
| | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China Research Institute of Subtropical Forestry, Chinese Academy of Forestry Hangzhou China
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Hangzhou 311400, China Zhejiang Key Laboratory of Forest Genetics and Breeding Hangzhou China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China Nanjing Forestry University Nanjing China
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Newfeld J, Ujimatsu R, Hiruma K. Uncovering the Host Range-Lifestyle Relationship in the Endophytic and Anthracnose Pathogenic Genus Colletotrichum. Microorganisms 2025; 13:428. [PMID: 40005793 PMCID: PMC11858739 DOI: 10.3390/microorganisms13020428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 02/12/2025] [Accepted: 02/13/2025] [Indexed: 02/27/2025] Open
Abstract
Colletotrichum includes agriculturally and scientifically important pathogens that infect numerous plants. They can also adopt an endophytic lifestyle, refraining from causing disease and/or even promoting plant growth when inoculated on a non-susceptible host. In this manner, the host range of a Colletotrichum fungus can shift, depending on whether it exhibits endophytic or pathogenic lifestyles. Some fungi, such as Colletotrichum tofieldiae, can even shift between pathogenicity and endophytism within the same host depending on the environmental conditions. Here, we aim to disentangle the relationship between lifestyle and host range in Colletotrichum. Specifically, we aim to demonstrate that lifestyle is dependent on the host colonized in many Colletotrichum fungi. We discuss the ways in which pathogenic Colletotrichum species may act endophytically on alternative hosts, how comparative genomics has uncovered candidate molecules (namely effectors, CAZymes, and secondary metabolites) underlying fungal lifestyle, and the merits of using endophytic fungi alongside pathogenic fungi in research, which facilitates the use of reverse genetics to uncover molecular determinants of lifestyle. In particular, we reference the Arabidopsis thaliana-Colletotrichum tofieldiae study system as a model for elucidating the dual roles of plant-fungus interactions, both endophytic and pathogenic, through integrative omics approaches and reverse genetics. This is because C. tofieldiae contains closely related pathogens and endophytes, making it an ideal model for identifying candidate determinants of lifestyle. This approach could identify key molecular targets for effective pathogen management in agriculture. Lastly, we propose a model in which pathogenic lifestyle occupies a different host range than the endophytic lifestyle. This will enhance our understanding of pathogenicity and endophytism in a globally significant fungal genus and lay the groundwork for future research examining molecular determinants of lifestyle in plant-associated fungi.
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Affiliation(s)
| | | | - Kei Hiruma
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan; (J.N.); (R.U.)
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7
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Al-Nijir M, Chuck CJ, Bedford MR, Henk DA. Metabolic modelling uncovers the complex interplay between fungal probiotics, poultry microbiomes, and diet. MICROBIOME 2024; 12:267. [PMID: 39707513 DOI: 10.1186/s40168-024-01970-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 11/07/2024] [Indexed: 12/23/2024]
Abstract
BACKGROUND The search for alternatives to antibiotic growth promoters in poultry production has increased interest in probiotics. However, the complexity of the interactions between probiotics, gut microbiome, and the host hinders the development of effective probiotic interventions. This study explores metabolic modelling to examine the possibility of designing informed probiotic interventions within poultry production. RESULTS Genomic metabolic models of fungi were generated and simulated in the context of poultry gut microbial communities. The modelling approach correlated with short-chain fatty acid production, particularly in the caecum. Introducing fungi to poultry microbiomes resulted in strain-specific and diet-dependent effects on the gut microbiome. The impact of fungal probiotics on microbiome diversity and pathogen inhibition varied depending on the specific strain, resident microbiome composition, and host diet. This context-dependency highlights the need for tailored probiotic interventions that consider the unique characteristics of each poultry production environment. CONCLUSIONS This study demonstrates the potential of metabolic modelling to elucidate the complex interactions between probiotics, the gut microbiome, and diet in poultry. While the effects of specific fungal strains were found to be context-dependent, the approach itself provides a valuable tool for designing targeted probiotic interventions. By considering the specific characteristics of the host microbiome and dietary factors, this methodology could guide the deployment of effective probiotics in poultry production. However, the current work relies on computational predictions, and further in vivo validation studies are needed to confirm the efficacy of the identified probiotic candidates. Nonetheless, this study represents a significant step in using metabolic models to inform probiotic interventions in the poultry industry. Video Abstract.
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Affiliation(s)
- Montazar Al-Nijir
- Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, UK
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | | | - Daniel A Henk
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK.
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Ollinger N, Malachová A, Schamann A, Sulyok M, Krska R, Weghuber J. Limited Effectiveness of Penicillium camemberti in Preventing the Invasion of Contaminating Molds in Camembert Cheese. Foods 2024; 13:2865. [PMID: 39335794 PMCID: PMC11431082 DOI: 10.3390/foods13182865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 09/03/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
Mold-ripened cheese acquires a distinctive aroma and texture from mold cultures that mature on a fresh cheese wheel. Owing to its high moisture content (aw = 0.95) and pliability, soft cheese is prone to contamination. Many contaminating mold species are unable to grow at colder temperatures, and the lactic acid produced by the cheese bacteria inhibits further infiltration. Thus, Camembert cheese is generally well protected against contamination by a wide range of species. In this study, cocultures of Penicillium camemberti and widely distributed mycotoxin-producing mold species were incubated on different types of agars, and purchased Camembert samples were deliberately contaminated with mycotoxin-producing mold species capable of growing at both 25 °C and 4 °C. The production of mycotoxins was then monitored by the extraction of the metabolites and their subsequent measurement by means of a liquid chromatography-tandem mass spectrometry (LC-MS/MS) based targeted metabolite profiling approach. The production of cyclopiazonic acid (CPA) was highly dependent on the species cocultivated with Penicillium camemberti, the temperature and the substrate. Contamination of Camembert cheese with Penicillium chrysogenum, Mucor hiemalis, or Penicillium glabrum induced CPA production at 25 °C. Although mold growth on cheese was not always evident on biofilms for certain cultures, except for Penicillium citrinum, which stained the monosaccharide agar yellow, mycotoxins were detected in many agar and cheese samples, as in all monosaccharide agar samples. In conclusion, cheese should be immediately discarded upon the first appearance of mold.
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Affiliation(s)
- Nicole Ollinger
- FFoQSI—Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Stelzhamerstr. 23, 4600 Wels, Austria
| | - Alexandra Malachová
- FFoQSI—Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Konrad Lorenz Str. 20, 3430 Tulln, Austria; (A.M.); (A.S.); (R.K.)
| | - Alexandra Schamann
- FFoQSI—Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Konrad Lorenz Str. 20, 3430 Tulln, Austria; (A.M.); (A.S.); (R.K.)
| | - Michael Sulyok
- Department for Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Str. 20, 3430 Tulln, Austria;
| | - Rudolf Krska
- FFoQSI—Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Konrad Lorenz Str. 20, 3430 Tulln, Austria; (A.M.); (A.S.); (R.K.)
- Department for Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Str. 20, 3430 Tulln, Austria;
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, University Road, Belfast BT7 1NN, UK
| | - Julian Weghuber
- FFoQSI—Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Stelzhamerstr. 23, 4600 Wels, Austria
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstrasse 23, 4600 Wels, Austria
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Zhao Y, Wang J, Xiao Q, Liu G, Li Y, Zha X, He Z, Kang J. New insights into decoding the lifestyle of endophytic Fusarium lateritium Fl617 via comparing genomes. Genomics 2024; 116:110925. [PMID: 39178998 DOI: 10.1016/j.ygeno.2024.110925] [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: 04/14/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
Fungal-plant interactions have persisted for 460 million years, and almost all terrestrial plants on Earth have endophytic fungi. However, the mechanism of symbiosis between endophytic fungi and host plants has been inconclusive. In this dissertation, we used a strain of endophytic Fusarium lateritium (Fl617), which was found in the previous stage to promote disease resistance in tomato, and selected the pathogenic Fusarium oxysporum Fo4287 and endophytic Fusarium oxysporum Fo47, which are in the same host and the closest relatives of Fl617, to carry out a comparative genomics analysis of the three systems and to provide a new perspective for the elucidation of the special lifestyle of the fungal endophytes. We found that endophytic F. lateritium has a smaller genome, fewer clusters and genes associated with pathogenicity, and fewer plant cell wall degrading enzymes (PCWDEs). There were also relatively fewer secondary metabolisms and typical Fusarium spp. toxins, and a lack of the key Fusarium spp. pathogenicity factor, secreted in xylem (SIX), but the endophytic fungi may be more sophisticated in their regulation of the colonization process. It is hypothesized that the endophytic fungi may have maintained their symbiosis with plants due to the relatively homogeneous microenvironment in plants for a long period of time, considering only plant interactions and discarding the relevant pathogenicity factors, and that their endophytic evolutionary tendency may tend to be genome streamlining and to enhance the fineness of the regulation of plant interactions, thus maintaining their symbiotic status with plants.
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Affiliation(s)
- Yan Zhao
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China
| | - Jiankang Wang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China
| | - Qing Xiao
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 550025, China
| | - Guihua Liu
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 550025, China
| | - Yongjie Li
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 550025, China
| | - Xingping Zha
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China
| | - Zhangjiang He
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China.
| | - Jichuan Kang
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China.
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Jaskolowski A, Poirier Y. Phosphate deficiency increases plant susceptibility to Botrytis cinerea infection by inducing the abscisic acid pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:828-843. [PMID: 38804074 DOI: 10.1111/tpj.16800] [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: 10/04/2023] [Accepted: 04/18/2024] [Indexed: 05/29/2024]
Abstract
Plants have evolved finely regulated defense systems to counter biotic and abiotic threats. In the natural environment, plants are typically challenged by simultaneous stresses and, amid such conditions, crosstalk between the activated signaling pathways becomes evident, ultimately altering the outcome of the defense response. As an example of combined biotic and abiotic stresses, inorganic phosphate (Pi) deficiency, common in natural and agricultural environments, can occur along with attack by the fungus Botrytis cinerea, a devastating necrotrophic generalist pathogen responsible for massive crop losses. We report that Pi deficiency in Arabidopsis thaliana increases its susceptibility to infection by B. cinerea by influencing the early stages of pathogen infection, namely spore adhesion and germination on the leaf surface. Remarkably, Pi-deficient plants are more susceptible to B. cinerea despite displaying the appropriate activation of the jasmonic acid and ethylene signaling pathways, as well as producing secondary defense metabolites and reactive oxygen species. Conversely, the callose deposition in response to B. cinerea infection is compromised under Pi-deficient conditions. The levels of abscisic acid (ABA) are increased in Pi-deficient plants, and the heightened susceptibility to B. cinerea observed under Pi deficiency can be reverted by blocking ABA biosynthesis. Furthermore, high level of leaf ABA induced by overexpression of NCED6 in Pi-sufficient plants also resulted in greater susceptibility to B. cinerea infection associated with increased spore adhesion and germination, and reduced callose deposition. Our findings reveal a link between the enhanced accumulation of ABA induced by Pi deficiency and an increased sensitivity to B. cinerea infection.
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Affiliation(s)
- Aime Jaskolowski
- Department of Plant Molecular Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, 1015, Lausanne, Switzerland
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11
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Inoue K, Tsuchida N, Saijo Y. Modulation of plant immunity and biotic interactions under phosphate deficiency. JOURNAL OF PLANT RESEARCH 2024; 137:343-357. [PMID: 38693461 DOI: 10.1007/s10265-024-01546-z] [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: 02/19/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024]
Abstract
Phosphorus (P) is an essential macronutrient for plant life and growth. P is primarily acquired in the form of inorganic phosphate (Pi) from soil. To cope with Pi deficiency, plants have evolved an elaborate system to improve Pi acquisition and utilization through an array of developmental and physiological changes, termed Pi starvation response (PSR). Plants also assemble and manage mutualistic microbes to enhance Pi uptake, through integrating PSR and immunity signaling. A trade-off between plant growth and defense favors the notion that plants lower a cellular state of immunity to accommodate host-beneficial microbes for nutrition and growth at the cost of infection risk. However, the existing data indicate that plants selectively activate defense responses against pathogens, but do not or less against non-pathogens, even under nutrient deficiency. In this review, we highlight recent advances in the principles and mechanisms with which plants balance immunity and growth-related processes to optimize their adaptation to Pi deficiency.
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Affiliation(s)
- Kanako Inoue
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara, 630-0192, Japan
| | - Natsuki Tsuchida
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara, 630-0192, Japan
| | - Yusuke Saijo
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara, 630-0192, Japan.
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12
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Damankeshan B, Shamshiri MH, Alaei H. Endophytic fungi are able to induce tolerance to salt stress in date palm seedlings (Phoenix dactylifera L.). Braz J Microbiol 2024; 55:759-775. [PMID: 38157149 PMCID: PMC10920517 DOI: 10.1007/s42770-023-01216-7] [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: 07/21/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
Date palm, typically considered a salinity-resistant plant, grows in arid and semi-arid regions worldwide, and experiences decreased growth and yields under salt stress. This study investigates the efficacy of endophytic fungi (EF) in enhancing the salinity tolerance of date palm seedlings. In this experiment, EF were isolated from date tree roots and identified morphologically. Following molecular identification, superior strains were selected to inoculate date palm seedlings (Phoenix dactylifera L., cv. Mazafati). The seedlings were subjected to varying levels of salinity stress for 4 months, utilizing a completely randomized factorial design with two factors: fungal strain type (six levels) and salinity stress (0, 100, 200, and 300 mM sodium chloride). The diversity analysis of endophytic fungi in date palm trees revealed that the majority of isolates belonged to the Ascomycota family, with Fusarium and Alternaria being the most frequently isolated genera. In this research, the application of fungal endophytes resulted in increased dry weight of roots, shoots, root length, plant height, and leaf number. Additionally, EF symbiosis with date palm seedling roots led to a reduction in sodium concentration and an increase in potassium and phosphorus concentrations in aerial parts under salt-stress conditions. While salinity elevated lipid peroxidation, consequently increasing malondialdehyde (MDA) levels, EF mitigated damage from reactive oxygen species (ROS) by enhancing antioxidant enzyme activity, including superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX), while promoting proline and total soluble sugar (TSS) accumulation. The colonization percentage generally increased with salinity stress intensity in most strains. According to the results, the application of EF can alleviate the adverse effects of salinity stress and enhance the growth of date palm seedlings under saline conditions.
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Affiliation(s)
- Bahareh Damankeshan
- Department of Horticultural Science, College of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran.
| | - Mohammad Hosein Shamshiri
- Department of Horticultural Science, College of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Hosein Alaei
- Department of Plant Pathology, College of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
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13
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Baroncelli R, Cobo-Díaz JF, Benocci T, Peng M, Battaglia E, Haridas S, Andreopoulos W, LaButti K, Pangilinan J, Lipzen A, Koriabine M, Bauer D, Le Floch G, Mäkelä MR, Drula E, Henrissat B, Grigoriev IV, Crouch JA, de Vries RP, Sukno SA, Thon MR. Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi. Gigascience 2024; 13:giae036. [PMID: 38940768 PMCID: PMC11212070 DOI: 10.1093/gigascience/giae036] [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: 08/31/2023] [Revised: 04/05/2024] [Accepted: 05/25/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes. RESULTS Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation. CONCLUSIONS These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.
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Affiliation(s)
- Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 40-50, 40127 Bologna, Italy
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, University of León, Campus Vegazana, 24007 León, Spain
| | - Tiziano Benocci
- Center for Health and Bioresources, Austrian Institute of Technology (AIT), Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Mao Peng
- Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Evy Battaglia
- Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sajeet Haridas
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - William Andreopoulos
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Kurt LaButti
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Jasmyn Pangilinan
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Maxim Koriabine
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Diane Bauer
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Gaetan Le Floch
- Laboratory of Biodiversity and Microbial Ecology (LUBEM), IBSAM, ESIAB, EA 3882, University of Brest, Technopôle Brest-Iroise, Parv. Blaise Pascal, 29280 Plouzané, France
| | - Miia R Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Siltavuorenpenger 5, 00170 Helsinki, Finland
| | - Elodie Drula
- UMR 7257, Architecture et Fonction des Macromolécules Biologiques, The French National Centre for Scientific Research (CNRS), University of Aix-Marseille (AMU), 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
- The French National Institute for Agricultural Research (INRA), USC 1408 AFMB, 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
| | - Bernard Henrissat
- UMR 7257, Architecture et Fonction des Macromolécules Biologiques, The French National Centre for Scientific Research (CNRS), University of Aix-Marseille (AMU), 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
- The French National Institute for Agricultural Research (INRA), USC 1408 AFMB, 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, 23453 Jeddah, Saudi Arabia
| | - Igor V Grigoriev
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Ave, MD 20705, Beltsville, USA
| | - Ronald P de Vries
- Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Serenella A Sukno
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
| | - Michael R Thon
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
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