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Stange P, Kersting J, Sivaprakasam Padmanaban PB, Schnitzler JP, Rosenkranz M, Karl T, Benz JP. The decision for or against mycoparasitic attack by Trichoderma spp. is taken already at a distance in a prey-specific manner and benefits plant-beneficial interactions. Fungal Biol Biotechnol 2024; 11:14. [PMID: 39252125 PMCID: PMC11384713 DOI: 10.1186/s40694-024-00183-4] [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: 05/29/2024] [Accepted: 08/23/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND The application of plant-beneficial microorganisms as bio-fertilizer and biocontrol agents has gained traction in recent years, as both agriculture and forestry are facing the challenges of poor soils and climate change. Trichoderma spp. are gaining popularity in agriculture and forestry due to their multifaceted roles in promoting plant growth through e.g. nutrient translocation, hormone production, induction of plant systemic resistance, but also direct antagonism of other fungi. However, the mycotrophic nature of the genus bears the risk of possible interference with other native plant-beneficial fungi, such as ectomycorrhiza, in the rhizosphere. Such interference could yield unpredictable consequences for the host plants of these ecosystems. So far, it remains unclear, whether Trichoderma is able to differentiate between plant-beneficial and plant-pathogenic fungi during the process of plant colonization. RESULTS We investigated whether Trichoderma spp. can differentiate between beneficial ectomycorrhizal fungi (represented by Laccaria bicolor and Hebeloma cylindrosporum) and pathogenic fungi (represented by Fusarium graminearum and Alternaria alternata) in different confrontation scenarios, including a newly developed olfactometer "race tube"-like system. Using two independent species, T. harzianum and T. atrobrunneum, with plant-growth-promoting and immune-stimulating properties towards Populus x canescens, our study revealed robustly accelerated growth towards phytopathogens, while showing a contrary response to ectomycorrhizal fungi. Transcriptomic analyses identified distinct genetic programs during interaction corresponding to the lifestyles, emphasizing the expression of mycoparasitism-related genes only in the presence of phytopathogens. CONCLUSION The findings reveal a critical mode of fungal community interactions belowground and suggest that Trichoderma spp. can distinguish between fungal partners of different lifestyles already at a distance. This sheds light on the entangled interactions of fungi in the rhizosphere and emphasizes the potential benefits of using Trichoderma spp. as a biocontrol agent and bio-fertilizer in tree plantations.
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Affiliation(s)
- Pia Stange
- Professorship for Fungal Biotechnology in Wood Science, Wood Research Munich, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Johannes Kersting
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | | | | | - Maaria Rosenkranz
- Research Unit Environmental Simulation, Helmholtz Munich, Neuherberg, Germany
- Institute of Plant Sciences, Ecology and Conservation Biology, University of Regensburg, Regensburg, Germany
| | - Tanja Karl
- Professorship for Fungal Biotechnology in Wood Science, Wood Research Munich, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - J Philipp Benz
- Professorship for Fungal Biotechnology in Wood Science, Wood Research Munich, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
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Zohair MM, Dongmei W, Shimizu K. Metabolic picture of microbial interaction: chemical crosstalk during co-cultivation between three dominant genera of bacteria and fungi in medicinal plants rhizosphere. Metabolomics 2024; 20:75. [PMID: 38980562 DOI: 10.1007/s11306-024-02138-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/06/2024] [Indexed: 07/10/2024]
Abstract
INTRODUCTION Microbial communities affect several aspects of the earth's ecosystem through their metabolic interaction. The dynamics of this interaction emerge from complex multilevel networks of crosstalk. Elucidation of this interaction could help us to maintain the balance for a sustainable future. OBJECTIVES To investigate the chemical language among highly abundant microbial genera in the rhizospheres of medicinal plants based on the metabolomic analysis at the interaction level. METHODS Coculturing experiments involving three microbial species: Aspergillus (A), Trichoderma (T), and Bacillus (B), representing fungi (A, T) and bacteria (B), respectively. These experiments encompassed various interaction levels, including dual cultures (AB, AT, TB) and triple cultures (ATB). Metabolic profiling by LC-QTOFMS revealed the effect of interaction level on the productivity and diversity of microbial specialized metabolites. RESULTS The ATB interaction had the richest profile, while the bacterial profile in the monoculture condition had the lowest. Two native compounds of the Aspergillus genus, aspergillic acid and the dipeptide asperopiperazine B, exhibited decreased levels in the presence of the AT interaction and were undetectable in the presence of bacteria during the interaction. Trichodermarin N and Trichodermatide D isolated from Trichoderma species exclusively detected during coexistence with bacteria (TB and ATB). These findings indicate that the presence of Bacillus activates cryptic biosynthetic gene clusters in Trichoderma. The antibacterial activity of mixed culture extracts was stronger than that of the monoculture extracts. The TB extract exhibited strong antifungal activity compared to the monoculture extract and other mixed culture treatments. CONCLUSION The elucidation of medicinal plant microbiome interaction chemistry and its effect on the environment will also be of great interest in the context of medicinal plant health Additionally, it sheds light on the content of bioactive constituents, and facilitating the discovery of novel antimicrobials.
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Affiliation(s)
- Moustafa M Zohair
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Research Institute, National Research Centre, Giza, 12622, Egypt
| | - Wang Dongmei
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kuniyoshi Shimizu
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan.
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González Y, Martínez-Soto D, de Los Santos-Villalobos S, Garcia-Marin LE, Juarez-Moreno K, Castro-Longoria E. Potential application of a fungal co-culture crude extract for the conservation of post-harvest fruits. Braz J Microbiol 2024; 55:1679-1691. [PMID: 38393617 PMCID: PMC11153422 DOI: 10.1007/s42770-024-01274-5] [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: 11/13/2023] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Fungal plant pathogens are responsible for serious losses in many economically important crop species worldwide. Due to the use of fungicides and the fungi genome plasticity, multi-drug resistant strains are emerging as a new generation of pathogens, causing an expansive range of superficial and systemic plant infections, or new opportunistic fungal pathogens for humans. The group of antagonistic fungi Trichoderma spp. has been widely used to enhance plant growth and for the control of different pathogens affecting crops. Although Neurospora crassa is not a mycoparasitic fungus, its secretion of secondary metabolites with antimicrobial activity has been described. In this work, the effect of crude extract of the monoculture of Trichoderma asperellum T8a or the co-culture with N. crassa as an inhibitory treatment against the fungal pathogens Botrytis cinerea and Fusarium solani was evaluated. The findings demonstrate that the secondary metabolites contained in the T. asperellum crude extract have a clear fungistatic activity against B. cinerea and F. solani. Interestingly, this fungistatic activity highly increases when T. asperellum is co-cultivated with the non-pathogenic fungus N. crassa. Moreover, the co-culture crude extract also showed antifungal activity on post-harvest fruits, and no toxic effects on Murine fibroblast L929 (CCL-1) and murine macrophages RAW 264.7 (TIB-71) were observed. All these results together are solid evidence of the potential of the co-culture crude extract of T. asperellum and N. crassa, as an antifungal agent against phytopathogenic fungi, or post-harvest fruits during the transportation or commercialization time.
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Affiliation(s)
- Yael González
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Carretera Tijuana-Ensenada 3918, Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - Domingo Martínez-Soto
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Carretera Tijuana-Ensenada 3918, Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | | | - Luis E Garcia-Marin
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Carretera Tijuana-Ensenada 3918, Zona Playitas, 22860, Ensenada, Baja California, Mexico
| | - Karla Juarez-Moreno
- Center for Applied Physics and Advanced Technology, UNAM. Blvd. Juriquilla 3001, Juriquilla La Mesa, 76230, Juriquilla, Queretaro, Mexico
| | - Ernestina Castro-Longoria
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Carretera Tijuana-Ensenada 3918, Zona Playitas, 22860, Ensenada, Baja California, Mexico.
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Silva GR, de Pina Cavalcanti F, Melo RM, Cintra E, Lima EM, Hamann PRV, do Vale LHF, Ulhoa CJ, Almeida F, Noronha EF. Extracellular vesicles from the mycoparasitic fungus Trichoderma harzianum. Antonie Van Leeuwenhoek 2024; 117:64. [PMID: 38565745 DOI: 10.1007/s10482-024-01958-w] [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: 12/30/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
Trichoderma harzianum is a filamentous fungus that can act as a mycoparasite, saprophyte, or a plant symbiotic. It is widely used as a biological control agent against phytopathogenic fungi and can also be used for plant growth promotion and biofortification. Interaction between T. harzianum and phytopathogenic fungi involves mycoparasitism, competition, and antibiosis. Extracellular vesicles (EVs) have been described as presenting a central role in mechanisms of communication and interaction among fungus and their hosts. In this study, we characterized extracellular vesicles of T. harzianum produced during growth in the presence of glucose or S. sclerotiorum mycelia. A set of vesicular proteins was identified using proteomic approach, mainly presenting predicted signal peptides.
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Affiliation(s)
- Gabrielle Rosa Silva
- Laboratory of Enzymology, Department of Cell Biology, University of Brasília, Brasilia, DF, 70910-900, Brazil
| | - Felipe de Pina Cavalcanti
- Laboratory of Enzymology, Department of Cell Biology, University of Brasília, Brasilia, DF, 70910-900, Brazil
| | - Reynaldo Magalhães Melo
- Laboratory of Enzymology, Department of Cell Biology, University of Brasília, Brasilia, DF, 70910-900, Brazil
| | - Emilio Cintra
- Faculty of Pharmacy, Laboratory of Pharmaceutical Technology, Lab. FarmaTec., Federal University of Goiás, 74690310, Goiânia, GO, Brazil
| | - Eliana Martins Lima
- Faculty of Pharmacy, Laboratory of Pharmaceutical Technology, Lab. FarmaTec., Federal University of Goiás, 74690310, Goiânia, GO, Brazil
| | - Pedro Ricardo Vieira Hamann
- São Carlos Institute of Physics, University of São Paulo, Avenida Trabalhador São-Carlense, 400, Parque Arnold Schimidt, São Carlos, SP, 13566-590, Brazil
| | - Luis H F do Vale
- Laboratory of Enzymology, Department of Cell Biology, University of Brasília, Brasilia, DF, 70910-900, Brazil
| | - Cirano José Ulhoa
- Biological Sciences Institute, University of Goias, Goiânia, 74690-900, GO, Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900, Brazil
| | - Eliane Ferreira Noronha
- Laboratory of Enzymology, Department of Cell Biology, University of Brasília, Brasilia, DF, 70910-900, Brazil.
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Wang Y, Wang J, Zhu X, Wang W. Genome and transcriptome sequencing of Trichoderma harzianum T4, an important biocontrol fungus of Rhizoctonia solani, reveals genes related to mycoparasitism. Can J Microbiol 2024; 70:86-101. [PMID: 38314685 DOI: 10.1139/cjm-2023-0148] [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: 02/07/2024]
Abstract
Trichoderma harzianum is a well-known biological control strain and a mycoparasite of Rhizoctonia solani. To explore the mechanisms of mycoparasitism, the genome and transcriptome of T. harzianum T4 were both assembled and analyzed in this study. The genome of T. harzianum T4 was assembled into 106 scaffolds, sized 41.25 Mb, and annotated with a total of 8118 predicted genes. We analyzed the transcriptome of T. harzianum T4 against R. solani in a dual culture in three culture periods: before contact (BC), during contact (C), and after contact (AC). Transcriptome sequencing identified 1092, 1222, and 2046 differentially expressed genes (DEGs), respectively. These DEGs, which are involved in pathogen recognition and signal transduction, hydrolase, transporters, antibiosis, and defense-related functional genes, are significantly upregulated in the mycoparasitism process. The results of genome and transcriptome analysis indicated that the mycoparasitism process of T. harzianum T4 was very complex. T. harzianum successfully recognizes and invades host cells and kills plant pathogens by regulating various DEGs at different culture periods. The relative expression levels of the 26 upregulated DEGs were confirmed by RT-qPCR to validate the reliability of the transcriptome data. The results provide insight into the molecular mechanisms underlying T. harzianum T4's mycoparasitic processes, and they provide a potential molecular target for the biological control mechanism of T. harzianum T4.
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Affiliation(s)
- Yaping Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiaochong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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Scott K, Konkel Z, Gluck-Thaler E, Valero David GE, Simmt CF, Grootmyers D, Chaverri P, Slot J. Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma. PLoS One 2023; 18:e0289280. [PMID: 38127903 PMCID: PMC10735191 DOI: 10.1371/journal.pone.0289280] [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: 03/24/2023] [Accepted: 07/14/2023] [Indexed: 12/23/2023] Open
Abstract
Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichoderma's diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.
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Affiliation(s)
- Kelsey Scott
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Emile Gluck-Thaler
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
| | | | - Coralie Farinas Simmt
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
| | - Django Grootmyers
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Priscila Chaverri
- Department of Natural Sciences, Bowie State University, Bowie, MD, United States of America
- School of Biology and Natural Products Research Center (CIPRONA), University of Costa Rica, San José, Costa Rica
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
- Center for Psychedelic Drug Research and Education, The Ohio State University, Columbus, OH, United States of America
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Wang Y, Wang J, Wang W. Identification of mycoparasitism-related genes in Trichoderma harzianum T4 that are active against Colletotrichum musae. Arch Microbiol 2023; 206:29. [PMID: 38117327 DOI: 10.1007/s00203-023-03767-7] [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: 10/17/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023]
Abstract
Trichoderma harzianum is a well-known biological control agent (BCA) that shows great potential in controlling many pathogenic fungi. To screen for genes associated with mycoparasitism, we sequenced and analyzed the transcriptome of T. harzianum T4 grown in dual culture with Colletotrichum musae. We analyzed differentially expressed genes (DEGs) of Trichoderma harzianum T4 in three different culture periods: before contact (BC), during contact (C) and after contact (AC). A total of 1453 genes were significantly differentially expressed compared to when T. harzianum T4 was cultured alone. During the three periods of double culture of T. harzianum T4 with C. musae, 74, 516, and 548 genes were up-regulated, respectively, and 11, 315, and 216 genes were down-regulated, respectively. The DEGs were screened using GO and KEGG enrichment analyses combined with differential expression multiples. Six gene categories related to mycoparasitism were screened: (a) pathogen recognition and signal transduction, (b) hydrolases, (c) ribosomal proteins and secreted proteins, (d) multidrug-resistant proteins and transporters, (e) heat shock proteins and detoxification, and (f) oxidative stress and antibiotics-related genes. The expression levels of 24 up-regulated genes during T. harzianum T4's antagonistic interaction with C. musae were detected via real-time fluorescence quantitative PCR (RT-qPCR). This study provided information on the transcriptional expression of T. harzianum T4 against C. musae. These results may help us to further understand the mechanism of mycoparasitism, which can provide a potential molecular target for improving the biological control capacity of T. harzianum T4.
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Affiliation(s)
- Yaping Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road No. 130, Shanghai, 200237, China
| | - Jian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road No. 130, Shanghai, 200237, China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road No. 130, Shanghai, 200237, China.
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Lv B, Zhao X, Guo Y, Li S, Sun M. Serine protease CrKP43 interacts with MAPK and regulates fungal development and mycoparasitism in Clonostachys chloroleuca. Microbiol Spectr 2023; 11:e0244823. [PMID: 37831480 PMCID: PMC10715147 DOI: 10.1128/spectrum.02448-23] [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: 06/11/2023] [Accepted: 09/04/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Mycoparasites play important roles in the biocontrol of plant fungal diseases, during which they secret multiple hydrolases such as serine proteases to degrade their fungal hosts. In this study, we demonstrated that the serine protease CrKP43 was involved in C. chloroleuca development and mycoparasitism with the regulation of Crmapk. To the best of our knowledge, it is the first report on the functions and regulatory mechanisms of serine proteases in C. chloroleuca. Our findings will provide new insight into the regulatory mechanisms of serine proteases in mycoparasites and contribute to clarifying the mechanisms underlying mycoparasitism of C. chloroleuca, which will facilitate the development of highly efficient fungal biocontrol agents as well.
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Affiliation(s)
- Binna Lv
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Zhao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shidong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manhong Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Tomah AA, Alamer ISA, Khattak AA, Ahmed T, Hatamleh AA, Al-Dosary MA, Ali HM, Wang D, Zhang J, Xu L, Li B. Potential of Trichoderma virens HZA14 in Controlling Verticillium Wilt Disease of Eggplant and Analysis of Its Genes Responsible for Microsclerotial Degradation. PLANTS (BASEL, SWITZERLAND) 2023; 12:3761. [PMID: 37960117 PMCID: PMC10649075 DOI: 10.3390/plants12213761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Verticillium dahliae is a soilborne fungal pathogen that causes vascular wilt diseases in a wide range of economically important crops, including eggplant. Trichoderma spp. are effective biological control agents that suppress a wide range of plant pathogens through a variety of mechanisms, including mycoparasitism. However, the molecular mechanisms of mycoparasitism of Trichoderma spp. in the degradation of microsclerotia of V. dahliae are not yet fully understood. In this study, the ability of 15 isolates of Trichoderma to degrade microsclerotia of V. dahliae was evaluated using a dual culture method. After 15 days, isolate HZA14 showed the greatest potential for microsclerotial degradation. The culture filtrate of isolate HZA14 also significantly inhibited the mycelial growth and conidia germination of V. dahliae at different dilutions. Moreover, this study showed that T. virens produced siderophores and indole-3-acetic acid (IAA). In disease control tests, T. virens HZA14 reduced disease severity in eggplant seedlings by up to 2.77%, resulting in a control efficacy of 96.59% at 30 days after inoculation. Additionally, inoculation with an HZA14 isolate increased stem and root length and fresh and dry weight, demonstrating plant growth promotion efficacy. To further investigate the mycoparasitism mechanism of T. virens HZA14, transcriptomics sequencing and real-time fluorescence quantitative PCR (RT-qPCR) were used to identify the differentially expressed genes (DEGs) of T. virens HZA14 at 3, 6, 9, 12, and 15 days of the interaction with microsclerotia of V. dahliae. In contrast to the control group, the mycoparasitic process of T. virens HZA14 exhibited differential gene expression, with 1197, 1758, 1936, and 1914 genes being up-regulated and 1191, 1963, 2050, and 2114 genes being down-regulated, respectively. Among these genes, enzymes associated with the degradation of microsclerotia, such as endochitinase A1, endochitinase 3, endo-1,3-beta-glucanase, alpha-N-acetylglucosaminidase, laccase-1, and peroxidase were predicted based on bioinformatics analysis. The RT-qPCR results confirmed the RNA-sequencing data, showing that the expression trend of the genes was consistent. These results provide important information for understanding molecular mechanisms of microsclerotial degradation and integrated management of Verticillium wilt in eggplant and other crops.
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Affiliation(s)
- Ali Athafah Tomah
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (A.A.T.); (I.S.A.A.); (A.A.K.); (T.A.); (J.Z.)
- Plant Protection, College of Agriculture, University of Misan, Al-Amarah 62001, Maysan Province, Iraq
| | - Iman Sabah Abd Alamer
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (A.A.T.); (I.S.A.A.); (A.A.K.); (T.A.); (J.Z.)
- Plant Protection, Agriculture Directorate, Al-Amarah 62001, Maysan Province, Iraq
| | - Arif Ali Khattak
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (A.A.T.); (I.S.A.A.); (A.A.K.); (T.A.); (J.Z.)
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (A.A.T.); (I.S.A.A.); (A.A.K.); (T.A.); (J.Z.)
- Xianghu Laboratory, Hangzhou 311231, China
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.); (H.M.A.)
| | - Munirah Abdullah Al-Dosary
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.); (H.M.A.)
| | - Hayssam M. Ali
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.); (H.M.A.)
| | - Daoze Wang
- Hangzhou Rural Revitalization Service Center, Hangzhou 310058, China;
| | - Jingze Zhang
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (A.A.T.); (I.S.A.A.); (A.A.K.); (T.A.); (J.Z.)
| | - Lihui Xu
- Institute of Eco-Environmental Protection, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (A.A.T.); (I.S.A.A.); (A.A.K.); (T.A.); (J.Z.)
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Al-Salihi SAA, Alberti F. Genomic Based Analysis of the Biocontrol Species Trichoderma harzianum: A Model Resource of Structurally Diverse Pharmaceuticals and Biopesticides. J Fungi (Basel) 2023; 9:895. [PMID: 37755004 PMCID: PMC10532697 DOI: 10.3390/jof9090895] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 09/28/2023] Open
Abstract
Fungi represents a rich repository of taxonomically restricted, yet chemically diverse, secondary metabolites that are synthesised via specific metabolic pathways. An enzyme's specificity and biosynthetic gene clustering are the bottleneck of secondary metabolite evolution. Trichoderma harzianum M10 v1.0 produces many pharmaceutically important molecules; however, their specific biosynthetic pathways remain uncharacterised. Our genomic-based analysis of this species reveals the biosynthetic diversity of its specialised secondary metabolites, where over 50 BGCs were predicted, most of which were listed as polyketide-like compounds associated clusters. Gene annotation of the biosynthetic candidate genes predicted the production of many medically/industrially important compounds including enterobactin, gramicidin, lovastatin, HC-toxin, tyrocidine, equisetin, erythronolide, strobilurin, asperfuranone, cirtinine, protoilludene, germacrene, and epi-isozizaene. Revealing the biogenetic background of these natural molecules is a step forward towards the expansion of their chemical diversification via engineering their biosynthetic genes heterologously, and the identification of their role in the interaction between this fungus and its biotic/abiotic conditions as well as its role as bio-fungicide.
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Affiliation(s)
| | - Fabrizio Alberti
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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11
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Castrillo ML, Bich GÁ, Amerio NS, Barengo MP, Zapata PD, Saparrat MCN, Villalba LL. Trichoderma koningiopsis (Hypocreaceae) has the smallest mitogenome of the genus Trichoderma. Front Microbiol 2023; 14:1141087. [PMID: 37383640 PMCID: PMC10294050 DOI: 10.3389/fmicb.2023.1141087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/24/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Fungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns. Methods The complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes. Results T. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers. Discussion The mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.
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Affiliation(s)
- María Lorena Castrillo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gustavo Ángel Bich
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia Soledad Amerio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcela Paola Barengo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mario Carlos Nazareno Saparrat
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Agrarias y Forestales, Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Instituto de Botánica Carlos Spegazzini, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Laura Lidia Villalba
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
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Xiao Z, Zhao Q, Li W, Gao L, Liu G. Strain improvement of Trichoderma harzianum for enhanced biocontrol capacity: Strategies and prospects. Front Microbiol 2023; 14:1146210. [PMID: 37125207 PMCID: PMC10134904 DOI: 10.3389/fmicb.2023.1146210] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
In the control of plant diseases, biocontrol has the advantages of being efficient and safe for human health and the environment. The filamentous fungus Trichoderma harzianum and its closely related species can inhibit the growth of many phytopathogenic fungi, and have been developed as commercial biocontrol agents for decades. In this review, we summarize studies on T. harzianum species complex from the perspective of strain improvement. To elevate the biocontrol ability, the production of extracellular proteins and compounds with antimicrobial or plant immunity-eliciting activities need to be enhanced. In addition, resistance to various environmental stressors should be strengthened. Engineering the gene regulatory system has the potential to modulate a variety of biological processes related to biocontrol. With the rapidly developing technologies for fungal genetic engineering, T. harzianum strains with increased biocontrol activities are expected to be constructed to promote the sustainable development of agriculture.
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Affiliation(s)
- Ziyang Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qinqin Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Li
- Shanghai Tobacco Group Beijing Cigarette Factory Co., Ltd., Beijing, China
| | - Liwei Gao
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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13
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Wang Y, Zhu X, Wang J, Shen C, Wang W. Identification of Mycoparasitism-Related Genes against the Phytopathogen Botrytis cinerea via Transcriptome Analysis of Trichoderma harzianum T4. J Fungi (Basel) 2023; 9:jof9030324. [PMID: 36983492 PMCID: PMC10055783 DOI: 10.3390/jof9030324] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Trichoderma harzianum is a well-known biological control agent (BCA) that is effective against a variety of plant pathogens. In previous studies, we found that T. harzianum T4 could effectively control the gray mold in tomatoes caused by Botrytis cinerea. However, the research on its biocontrol mechanism is not comprehensive, particularly regarding the mechanism of mycoparasitism. In this study, in order to further investigate the mycoparasitism mechanism of T. harzianum T4, transcriptomic sequencing and real-time fluorescence quantitative PCR (RT-qPCR) were used to identify the differentially expressed genes (DEGs) of T. harzianum T4 at 12, 24, 48 and 72 h of growth in the cell wall of B. cinerea (BCCW) or a sucrose medium. A total of 2871 DEGs and 2148 novel genes were detected using transcriptome sequencing. Through GO and KEGG enrichment analysis, we identified genes associated with mycoparasitism at specific time periods, such as encoding kinases, signal transduction proteins, carbohydrate active enzymes, hydrolytic enzymes, transporters, antioxidant enzymes, secondary metabolite synthesis, resistance proteins, detoxification genes and genes associated with extended hyphal longevity. To validate the transcriptome data, RT-qCPR was performed on the transcriptome samples. The RT-qPCR results show that the expression trend of the genes was consistent with the RNA-Seq data. In order to validate the screened genes associated with mycoparasitism, we performed a dual-culture antagonism test on T. harzianum and B. cinerea. The results of the dual-culture RT-qPCR showed that 15 of the 24 genes were upregulated during and after contact between T. harzianum T4 and B. cinerea (the same as BCCW), which further confirmed that these genes were involved in the mycoparasitism of T. harzianum T4. In conclusion, the transcriptome data provided in this study will not only improve the annotation information of gene models in T. harzianum T4 genome, but also provide important transcriptome information regarding the process of mycoparasitism at specific time periods, which can help us to further understand the mechanism of mycoparasitism, thus providing a potential molecular target for T. harzianum T4 as a biological control agent.
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Affiliation(s)
- Yaping Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaochong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chao Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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14
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Wang Y, Chen H, Ma L, Gong M, Wu Y, Bao D, Zou G. Use of CRISPR-Cas tools to engineer Trichoderma species. Microb Biotechnol 2022; 15:2521-2532. [PMID: 35908288 PMCID: PMC9518982 DOI: 10.1111/1751-7915.14126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022] Open
Abstract
Given their lignocellulose degradability and biocontrol activities, fungi of the ubiquitously distributed genus Trichoderma have multiple industrial and agricultural applications. Genetic manipulation plays a valuable role in tailoring novel engineered strains with enhanced target traits. Nevertheless, as applied to fungi, the classic tools of genetic manipulation tend to be time-consuming and tedious. However, the recent development of the CRISPR-Cas system for gene editing has enabled researchers to achieve genome-wide gene disruptions, gene replacements, and precise editing, and this technology has emerged as a primary focus for novel developments in engineered strains of Trichoderma. Here, we provide a brief overview of the traditional approaches to genetic manipulation, the different strategies employed in establishing CRSIPR-Cas systems, the utilization of these systems to develop engineered strains of Trichoderma for desired applications, and the future trends in biotechnology.
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Affiliation(s)
- Ying Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
| | - Hongyu Chen
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
| | - Liang Ma
- Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural SciencesZhejiang A&F UniversityLin'an HangzhouChina
| | - Ming Gong
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
| | - Yingying Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
| | - Dapeng Bao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
| | - Gen Zou
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
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15
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Lopes da Silva F, Aquino EN, Costa da Cunha D, Vieira Hamann PR, Magalhães TB, Steindorff AS, Ulhoa CJ, Noronha EF. Analysis of Trichoderma harzianum TR 274 secretome to assign candidate proteins involved in symbiotic interactions with Phaseolus vulgaris. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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ATP-Binding Cassette (ABC) Transporters in Fusarium Specific Mycoparasite Sphaerodes mycoparasitica during Biotrophic Mycoparasitism. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12157641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent transcriptomic profiling has revealed importance membrane transporters such as ATP-binding cassette (ABC) transporters in fungal necrotrophic mycoparasites. In this study, RNA-Seq allowed rapid detection of ABC transcripts involved in biotrophic mycoparasitism of Sphaerodes mycoparasitica against the phytopathogenic and mycotoxigenic Fusarium graminearum host, the causal agent of Fusarium head blight (FHB). Transcriptomic analyses of highly expressed S. mycoparasitica genes, and their phylogenetic relationships with other eukaryotic fungi, portrayed the ABC transporters’ evolutionary paths towards biotrophic mycoparasitism. Prior to the in silico phylogenetic analyses, transmission electron microscopy (TEM) was used to confirm the formation of appressorium/haustorium infection structures in S. mycoparasitica during early (1.5 d and 3.5 d) stages of mycoparasitism. Transcripts encoding biotrophy-associated secreted proteins did uncover the enrolment of ABC transporter genes in this specific biocontrol mode of action, while tandem ABC and BUB2 (non-ABC) transcripts seemed to be proper for appressorium development. The next-generation HiSeq transcriptomic profiling of the mycoparasitic hypha samples, revealed 81 transcripts annotated to ABC transporters consisting of a variety of ABC-B (14%), ABC-C (22%), and ABC-G (23%), and to ABC-A, ABC-F, aliphatic sulfonates importer (TC 3.A.1.17.2), BtuF, ribose importer (TC 3.A.1.2.1), and unknown families. The most abundant transcripts belonged to the multidrug resistance exporter (TC 3.A.1.201) subfamily of the ABC-B family, the conjugate transporter (TC 3.A.1.208) subfamily of the ABC-C family, and the pleiotropic drug resistance (PDR) (TC 3.A.1.205) subfamily of the ABC-G family. These findings highlight the significance of ABC transporter genes that control cellular detoxification against toxic substances (e.g., chemical pesticides and mycotoxins) in sustaining a virulence of S. mycoparasitica for effective biotrophic mycoparasitism on the F. graminearum host. The findings of this study provide clues to better understand the biotrophic mycoparasitism of S. mycoparasitica interacting with the Fusarium host, which implies that the ABC transporter group of key proteins is involved in the mycoparasite’s virulence and multidrug resistance to toxic substances including cellular detoxification.
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17
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Asad SA. Mechanisms of action and biocontrol potential of Trichoderma against fungal plant diseases - A review. ECOLOGICAL COMPLEXITY 2022. [DOI: 10.1016/j.ecocom.2021.100978] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Yang M, Zhang W, Lv Z, Shi L, Zhang K, Ge B. Evaluation of the Inhibitory Effects of Wuyiencin, a Secondary Metabolite of Streptomyces albulus CK-15, Against Sclerotinia sclerotiorum In Vitro. PLANT DISEASE 2022; 106:156-164. [PMID: 34184553 DOI: 10.1094/pdis-05-21-0987-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sclerotinia sclerotiorum (Lib.) de Bary, a destructive fungal pathogen with an extensive host range, causes various diseases with the potential to cause huge economic losses to crops worldwide. Streptomyces species produce secondary metabolites with variable structures and biological activities that offer possible control methods for crop diseases. Herein, we evaluated the inhibitory effects of wuyiencin, a secondary metabolite of Streptomyces albulus CK-15, against S. sclerotiorum. The results showed that wuyiencin markedly inhibited mycelial growth and germination and the formation of sclerotia. It also increased cell membrane permeability, resulting in leakage of intracellular substances in pathogen mycelia. Wuyiencin markedly decreased oxalic acid content and the activities of polygalacturonase and pectin methyl-galacturonic enzymes. Moreover, it downregulated Nox1, ITL, pph1, Caf1, and sca1, all genes related to growth and infection. Lesions were smaller and less pronounced on soybean (Glycine max [L.] Merr.) leaves pretreated with wuyiencin in vitro, and the inhibition rate reached 78.36%. The results suggest that wuyiencin holds promise for the management of diseases caused by S. sclerotiorum, and the findings provide clues on the mechanism of action.
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Affiliation(s)
- Miaoling Yang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Wei Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Zhaoyang Lv
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Liming Shi
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Kecheng Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Beibei Ge
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
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María Fernanda Villarreal-Delgado, Parra-Cota FI, Cira-Chávez LA, Estrada-Alvarado MI, de los Santos-Villalobos S. Bacillus sp. FSQ1: a Promising Biological Control Agent Against Sclerotinia sclerotiorum, the Causal Agent of white Mold in Common Bean (Phaseolus vulgaris L.). BIOL BULL+ 2021. [DOI: 10.1134/s1062359021060182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Piombo E, Vetukuri RR, Broberg A, Kalyandurg PB, Kushwaha S, Funck Jensen D, Karlsson M, Dubey M. Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions. Microbiol Spectr 2021; 9:e0109921. [PMID: 34549988 PMCID: PMC8557909 DOI: 10.1128/spectrum.01099-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Dicer-like proteins (DCLs) play a vital role in RNA interference (RNAi), by cleaving RNA filament into small RNAs. Although DCL-mediated RNAi can regulate interspecific communication between pathogenic/mutualistic organisms and their hosts, its role in mycoparasitic interactions is yet to be investigated. In this study, we deleted dcl genes in the mycoparasitic fungus Clonostachys rosea and characterize the functions of DCL-dependent RNAi in mycoparasitism. Deletion of dcl2 resulted in a mutant with reduced secondary metabolite production, antagonism toward the plant-pathogenic fungus Botrytis cinerea, and reduced ability to control Fusarium foot rot disease on wheat, caused by Fusarium graminearum. Transcriptome sequencing of the in vitro interaction between the C. rosea Δdcl2 strain and B. cinerea or F. graminearum identified the downregulation of genes coding for transcription factors, membrane transporters, hydrolytic enzymes, and secondary metabolites biosynthesis enzymes putatively involved in antagonistic interactions, in comparison with the C. rosea wild-type interaction. A total of 61 putative novel microRNA-like RNAs (milRNAs) were identified in C. rosea, and 11 were downregulated in the Δdcl2 mutant. In addition to putative endogenous gene targets, these milRNAs were predicted to target B. cinerea and F. graminearum virulence factor genes, which showed an increased expression during interaction with the Δdcl2 mutant incapable of producing the targeting milRNAs. In summary, this study constitutes the first step in elucidating the role of RNAi in mycoparasitic interactions, with important implications for biological control of plant diseases, and poses the base for future studies focusing on the role of cross-species RNAi regulating mycoparasitic interactions. IMPORTANCE Small RNAs mediated RNA interference (RNAi) known to regulate several biological processes. Dicer-like endoribonucleases (DCLs) play a vital role in the RNAi pathway by generating sRNAs. In this study, we investigated a role of DCL-mediated RNAi in interference interactions between mycoparasitic fungus Clonostachys rosea and the two fungal pathogens Botrytis cinerea and Fusarium graminearum (here called mycohosts). We found that the dcl mutants were not able to produce 11 sRNAs predicted to finetune the regulatory network of genes known to be involved in production of hydrolytic enzymes, antifungal compounds, and membrane transporters needed for antagonistic action of C. rosea. We also found C. rosea sRNAs putatively targeting known virulence factors in the mycohosts, indicating RNAi-mediated cross-species communication. Our study expanded the understanding of underlying mechanisms of cross-species communication during interference interactions and poses a base for future works studying the role of DCL-based cross-species RNAi in fungal interactions.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ramesh R. Vetukuri
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pruthvi B. Kalyandurg
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Sandeep Kushwaha
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Zhang D, Yu J, Ma C, Kong L, He C, Li J. Genomic Analysis of the Mycoparasite Pestalotiopsis sp. PG52. Pol J Microbiol 2021; 70:189-199. [PMID: 34349810 PMCID: PMC8326988 DOI: 10.33073/pjm-2021-016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/06/2021] [Indexed: 11/25/2022] Open
Abstract
Pestalotiopsis sp. is a mycoparasite of the plant pathogen Aecidium wenshanense. To further understand the mycoparasitism mechanism of Pestalotiopsis sp., we assembled and analyzed its genome. The genome of Pestalotiopsis sp. strain PG52 was assembled into 335 scaffolds and had a size of 58.01 Mb. A total of 20,023 predicted genes and proteins were annotated. This study compared PG52 with the mycoparasites Trichoderma harzianum, Trichoderma atroviride, and Trichoderma virens. This study reveals the entirely different mycoparasitism mechanism of Pestalotiopsis compared to Trichoderma and reveals this mycoparasite’s strong ability to produce secondary metabolites.
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Affiliation(s)
- Dengyun Zhang
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Jinde Yu
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Changle Ma
- School of Landscape Architecture and Horticulture Science, Southwest Forestry University, Kunming, China
| | - Lei Kong
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Chengzhong He
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Jing Li
- College of Life Science, Southwest Forestry University, Kunming, China
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Peng X, Wu B, Zhang S, Li M, Jiang X. Transcriptome Dynamics Underlying Chlamydospore Formation in Trichoderma virens GV29-8. Front Microbiol 2021; 12:654855. [PMID: 34168625 PMCID: PMC8217873 DOI: 10.3389/fmicb.2021.654855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 05/03/2021] [Indexed: 11/15/2022] Open
Abstract
Trichoderma spp. are widely used biocontrol agents which are antagonistic to a variety of plant pathogens. Chlamydospores are a type of propagules produced by many fungi that have thick walls and are highly resistant to adverse environmental conditions. Chlamydospore preparations of Trichoderma spp. can withstand various storage conditions, have a longer shelf life than conidial preparations and have better application potential. However, large-scale production of chlamydospores has proven difficult. To understand the molecular mechanisms governing chlamydospore formation (CF) in Trichoderma fungi, we performed a comprehensive analysis of transcriptome dynamics during CF across 8 different developmental time points, which were divided into 4 stages according to PCA analysis: the mycelium growth stage (S1), early and middle stage of CF (S2), flourishing stage of CF (S3), and late stage of CF and mycelia initial autolysis (S4). 2864, 3206, and 3630 DEGs were screened from S2 vs S1, S3 vs S2, and S4 vs S3, respectively. We then identified the pathways and genes that play important roles in each stage of CF by GO, KEGG, STC and WGCNA analysis. The results showed that DEGs in the S2 vs S1 were mainly enriched in organonitrogen compound metabolism, those in S3 vs S2 were mainly involved in secondary metabolite, cell cycle, and N-glycan biosynthesis, and DEGs in S4 vs S3 were mainly involved in lipid, glycogen, and chitin metabolic processes. We speculated that mycelial assimilation and absorption of exogenous nitrogen in the early growth stage (S1), resulted in subsequent nitrogen deficiency (S2). At the same time, secondary metabolites and active oxygen free radicals released during mycelial growth produced an adverse growth environment. The resulting nitrogen-deficient and toxin enriched medium may stimulate cell differentiation by initiating cell cycle regulation to induce morphological transformation of mycelia into chlamydospores. High expression of genes relating to glycogen, lipid, mannan, and chitin synthetic metabolic pathways during the flourishing (S3) and late stages (S4) of CF may be conducive to energy storage and cell wall construction in chlamydospores. For further verifying the functions of the amino sugar and nucleotide sugar metabolism (tre00520) pathway in the CF of T. virens GV29-8 strain, the chitin synthase gene (TRIVIDRAFT_90152), one key gene of the pathway, was deleted and resulted in the dysplasia of mycelia and an incapability to form normal chlamydospores, which illustrated the pathway affecting the CF of T. virens GV29-8 strain. Our results provide a new perspective for understanding the genetics of biochemical pathways involved in CF of Trichoderma spp.
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Affiliation(s)
| | | | | | - Mei Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiliang Jiang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Wu B, Cox MP. Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi. Environ Microbiol 2021; 23:3251-3264. [PMID: 33939870 PMCID: PMC8360070 DOI: 10.1111/1462-2920.15554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/13/2022]
Abstract
Fungi have evolved diverse lifestyles and adopted pivotal new roles in both natural ecosystems and human environments. However, the molecular mechanisms underlying their adaptation to new lifestyles are obscure. Here, we hypothesize that genes shared across all species with the same lifestyle, but absent in genera with alternative lifestyles, are crucial to that lifestyle. By analysing dozens of species within four genera in a fungal order, with each genus following a different lifestyle, we find that genus-specific genes are typically few in number. Notably, not all genus-specific genes appear to derive from de novo birth, with most instead reflecting recurrent loss across the fungi. Importantly, however, a subset of these genus-specific genes are shared by fungi with the same lifestyle in quite different evolutionary orders, thus supporting the view that some genus-specific genes are necessary for specific lifestyles. These lifestyle-specific genes are enriched for key functional classes and often exhibit specialized expression patterns. Genus-specific selection also contributes to lifestyle transitions, and is especially associated with intensity of pathogenesis. Our study, therefore, suggests that fungal adaptation to new lifestyles often requires just a small number of core genes, with gene turnover and positive selection playing complementary roles.
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Affiliation(s)
- Baojun Wu
- Statistics and Bioinformatics Group, School of Fundamental SciencesMassey UniversityPalmerston North4410New Zealand
- Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Murray P. Cox
- Statistics and Bioinformatics Group, School of Fundamental SciencesMassey UniversityPalmerston North4410New Zealand
- Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
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Liu H, Wang H, Lu X, Xiao C, Peng B, Zhou Q. Molecular characterization of a novel single-stranded RNA virus, ChRV1, isolated from the plant-pathogenic fungus Colletotrichum higginsianum. Arch Virol 2021; 166:1805-1809. [PMID: 33956246 DOI: 10.1007/s00705-021-05071-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/01/2021] [Indexed: 10/21/2022]
Abstract
In this study, a novel single-stranded RNA virus was isolated from the plant-pathogenic fungus Colletotrichum higginsianum strain HTC-5, and the virus was named "Colletotrichum higginsianum ssRNA virus 1" (ChRV1). The complete genome of ChRV1 is 3850 nucleotides in length with a GC content of 52% and contains two in-frame open reading frames (ORFs): ORF1 (smaller) and ORF2 (larger). ORF1 encodes a protein with the highest sequence similarity to proteins encoded by Phoma matteucciicola RNA virus 1 (PmRV1, 47.99% identity) and Periconia macrospinosa ambiguivirus 1 (PmAV1, 50.73% identity). ORF2 encodes a protein with a conserved RNA-dependent RNA polymerase (RdRp) domain with similarity to the RdRps of PmRV1 (61.41% identity) and PmAV1 (60.61% identity), which are recently reported unclassified (+) ssRNA mycoviruses. Phylogenetic analysis of the RdRp domain showed that ChRV1 grouped together with PmRV1, PmAV1, and other unclassified (+) ssRNA mycoviruses and had a distant relationship to invertebrate viruses and plant viruses of the family Tombusviridae. This is the first report of a novel (+) ssRNA virus infecting the phytopathogenic fungus C. higginsianum.
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Affiliation(s)
- Hong Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Hui Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Xun Lu
- Agricultural Science Institute of Xiang Xi Tujia and Miao Autonomous Prefecture, Xiangxi, 416000, China
| | - Cheng Xiao
- Agricultural Science Institute of Xiang Xi Tujia and Miao Autonomous Prefecture, Xiangxi, 416000, China
| | - Bo Peng
- Agricultural Science Institute of Xiang Xi Tujia and Miao Autonomous Prefecture, Xiangxi, 416000, China
| | - Qian Zhou
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China.
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Darshan K, Aggarwal R, Bashyal BM, Singh J, Shanmugam V, Gurjar MS, Solanke AU. Transcriptome Profiling Provides Insights Into Potential Antagonistic Mechanisms Involved in Chaetomium globosum Against Bipolaris sorokiniana. Front Microbiol 2020; 11:578115. [PMID: 33365017 PMCID: PMC7750538 DOI: 10.3389/fmicb.2020.578115] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/30/2020] [Indexed: 11/13/2022] Open
Abstract
Chaetomium globosum Kunze is recognized as a potential biocontrol fungus against spot blotch of wheat caused by Bipolaris sorokiniana. Its molecular mechanism of biocontrol activity and the biosynthetic pathways involved have not been yet elucidated. Here, global transcriptome profiling of C. globosum strain Cg2 during interaction with B. sorokiniana isolate BS112 using RNA-seq was performed in order to gain insights into the potential mechanisms of antagonism. The Illumina HiSeq platform (2 × 150 bp) yielded an average of 20-22 million reads with 50-58% GC. De novo assembly generated 45,582 transcripts with 27,957 unigenes. Transcriptome analysis displayed distinct expression profiles in the interaction (Cg2-BS112), out of which 6,109 unique differentially expressed genes were present. The predominant transcripts classified as genes involved in "catalytic activity" constituted 45.06%, of which 10.02% were associated with "hydrolytic activity" (GO:0008152), and similarly, in the biological process, 29.18% of transcripts were involved in "metabolic activity" (GO:0004096 and GO:0006979). Heat map and cluster categorization suggested an increase in the expression levels of genes encoding secondary metabolites like polyketide synthase (GO:0009058), S-hydroxymethyl glutathione dehydrogenase (GO:0006069), terpene cyclase (EC 4.2.3.-), aminotran_1_2 domain-containing protein (GO:0009058), and other hydrolytic CAZYmes such as the glycosyl hydrolase (GH) family (GH 13, GH 2, GH 31, and GH 81; GO:0005975), cellulase domain-containing protein, chitinases, β-1, 3-glucanases (GO:0004565), glucan endo-1,3-beta-glucanase (GO:0052861), and proteases (GO:0004177). The obtained RNA-seq data were validated by RT-qPCR using 20 randomly chosen genes, showing consistency with the RNA-seq results. The present work is worldwide the first effort to unravel the biocontrol mechanism of C. globosum against B. sorokiniana. It generated a novel dataset for further studies and facilitated improvement of the gene annotation models in the C. globosum draft genome.
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Affiliation(s)
- K. Darshan
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
| | - Rashmi Aggarwal
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
| | - Bishnu Maya Bashyal
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
| | - Jagmohan Singh
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
| | - V. Shanmugam
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
| | - Malkhan S. Gurjar
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi, India
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Zhang X, Xu J, Muhayimana S, Xiong H, Liu X, Huang Q. Antifungal effects of 3-(2-pyridyl)methyl-2-(4-chlorphenyl) iminothiazolidine against Sclerotinia sclerotiorum. PEST MANAGEMENT SCIENCE 2020; 76:2978-2985. [PMID: 32246520 DOI: 10.1002/ps.5843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/16/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum threatens oilseed rape cultivation, and the emergence of fungicide-resistant strains has led to control failures worldwide. Identifying novel chemical alternatives with different modes of action and high antifungal activities is thus crucial. Herein we evaluated the antifungal effects of 3-(2-pyridyl)methyl-2-(4-chlorphenyl)imino- thiazolidine (PMAS) on S. sclerotiorum to determine its efficacy for SSR management. RESULTS PMAS had an inhibitory effect on mycelial growth; the EC50 values were 17.83 and 21.15 μg mL-1 for the carbendazim-susceptible strain Ss01 and carbendazim-resistant strain Hm25, respectively. PMAS treatment changed the color of inhibited mycelia to green, and the hyphae were sustained in the undifferentiated stage. Cysteine supplementation made this green color disappear, whereas methionine enhanced the color. Moreover, PMAS treatment markedly inhibited oxalic acid biogenesis, increased free thiol content in mycelia, and weakened the activities of oxaloacetase and malate dehydrogenase, but had little effect on the activity of glyoxylate dehydrogenase. Cysteine could reverse the inhibitory effects of PMAS on mycelial morphogenesis and biochemical constituents, except thiol production. In the pot-culture experiment, PMAS showed a good protective effect, with the control efficacy being >91% on SSR. CONCLUSION PMAS appears to be an effective fungicide for SSR management. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Xianfei Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Jiuyong Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Solange Muhayimana
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Hui Xiong
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Xuefeng Liu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Qingchun Huang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
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27
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Stummer BE, Zhang Q, Zhang X, Warren RA, Harvey PR. Quantification of Trichoderma afroharzianum, Trichoderma harzianum and Trichoderma gamsii inoculants in soil, the wheat rhizosphere and in planta suppression of the crown rot pathogen Fusarium pseudograminearum. J Appl Microbiol 2020; 129:971-990. [PMID: 32320112 DOI: 10.1111/jam.14670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 04/02/2020] [Accepted: 04/16/2020] [Indexed: 11/29/2022]
Abstract
AIMS Develop quantitative assays (qPCR) to determine the detection threshold limits, colonization and persistence of Trichoderma gamsii, Trichoderma afroharzianum and T. harzianum inoculants in cropping soils, the wheat rhizosphere and their in planta suppressive efficacy against the crown rot pathogen Fusarium pseudograminearum. METHODS AND RESULTS Trichoderma qPCR primers were designed from the internal transcribed spacer region of 5.8S rDNA and from sequences of DNA fragments diagnostic for each inoculant genotype. The minimum detection thresholds of qPCR assays varied between 1 × 103 (log 3) and 8 × 104 (log 4·9) conidia (genome) equivalents per gram of soil for multi- and single-copy target sequences, respectively and were independent of soil type. There was a strong correlation (r > 0·974) between culture-dependent and culture-independent (qPCR) quantification methods. In wheat bioassays, Trichoderma inoculants colonized rhizosphere soils and wheat roots at 56-112 days postemergence to a depth of 20 cm but were more abundant (P < 0·001) at 0-10 cm root depth, means ranging from 2 × 102 (log 2·3) to 4 × 105 (log 5·6) conidia equivalents per gram of rhizosphere soil or root tissue. Inoculants reduced (P < 0·001) F. pseudograminearum biomass in wheat crown and root tissue by up to 5754-fold and increased (P = 0·008) plant biomass, relative to the pathogen control. CONCLUSIONS The qPCR assays provided sensitive and accurate assessment of wheat root and rhizosphere soil colonization of Trichoderma inoculants. Strains persisted through to grain maturity at levels shown to significantly suppress F. pseudograminearum in planta. SIGNIFICANCE AND IMPACT OF THE STUDY The qPCR assays developed here were used to determine the wheat rhizosphere dynamics of T. harzianum, T. afroharzianum and T. gamsii inoculants and their suppressive efficacy against F. pseudograminearum in planta. These assays can be applied to monitor inoculant dynamics in suppressing crown rot and other wheat root diseases in the field.
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Affiliation(s)
- B E Stummer
- CSIRO Agriculture and Food, Glen Osmond, SA, Australia
| | - Q Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - X Zhang
- Ecology Research Institute, Shandong Academy of Sciences, Jinan, Shandong, China
| | - R A Warren
- CSIRO Agriculture and Food, Glen Osmond, SA, Australia
| | - P R Harvey
- CSIRO Agriculture and Food, Glen Osmond, SA, Australia.,Ecology Research Institute, Shandong Academy of Sciences, Jinan, Shandong, China
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28
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Heshof R, Visscher B, van de Zilver E, van de Vondervoort R, van Keulen F, Delahaije RJBM, Wind RD. Production of tailor-made enzymes to facilitate lipid extraction from the oleaginous yeast Schwanniomyces occidentalis. AMB Express 2020; 10:41. [PMID: 32112299 PMCID: PMC7048881 DOI: 10.1186/s13568-020-00974-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/19/2020] [Indexed: 12/18/2022] Open
Abstract
Due to the depletion of fossil fuel resources and concern about increasing atmospheric CO2 levels, the production of microbial oil as source for energy and chemicals is considered as a sustainable alternative. A promising candidate strain for the production of microbial oil is the oleaginous yeast Schwanniomyces occidentalis CBS 2864. To compete with fossil resources, cultivation and processing of S. occidentalis requires improvement. Currently, different cell wall disruption techniques based on mechanical, chemical, physiological, and biological methods are being investigated using a variety of oil producing yeasts and microalgae. Most of these techniques are not suitable for upscaling because they are technically or energetically unfavorable. Therefore, new techniques have to be developed to overcome this challenge. Here, we demonstrate an effective mild enzymatic approach for cell disruption to facilitate lipid extraction from the oleaginous yeast S. occidentalis. Most oil was released by applying 187 mg L−1 tailor-made enzymes from Trichoderma harzianum CBS 146429 against the yeast cell wall of S. occidentalis at pH 5.0 and 40 °C with 4 h of incubation time after applying 1 M NaOH as a pretreatment step.
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29
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Rabinal C, Bhat S. Identification of Differentially Expressed Genes in Trichoderma koningii IABT1252 During Its Interaction with Sclerotium rolfsii. Curr Microbiol 2019; 77:396-404. [PMID: 31844935 DOI: 10.1007/s00284-019-01838-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
Sclerotium rolfsii, a soil-borne fungal pathogen, infects more than 500 crop species and causes stem rot/collar rot/seed rot/southern blight/wilt in a wide variety of crops which results in significant yield loses. Presently, antagonistic microbes are gaining more importance in managing plant pathogens because they control the pathogen in an environment-friendly manner. Trichoderma is an antagonistic fungi and most popularly used biocontrol agent against phytopathogenic fungi. It is predominantly used to treat soil and seed for the control of Sclerotium rolfsii infestation. In this study, the Trichoderma koningii IABT1252 that performed better in controlling groundnut seed/ seedling rot caused by S. rolfsii in pot experiments were selected to know the molecular basis for the control. Differentially expressed genes in Trichoderma at two different stages of interaction (prior to contact and after contact with S. rolfsii) were identified. In both the stages, some of the differentially expressed genes included ones coding for hydrolytic enzymes, secondary metabolite biosynthesis, transcription factors, signaling proteins, transporter proteins, and proteins involved in mycoparasitic process of Trichoderma.
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Affiliation(s)
- Chidanand Rabinal
- Department of Biotechnology, College of Agriculture, UAS Dharwad, Karnataka, 580005, India.
| | - Sumangala Bhat
- Department of Genetics and Plant Breeding, College of Agriculture, UAS Dharwad, Karnataka, 580005, India
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30
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Eisermann I, Weihmann F, Krijger JJ, Kröling C, Hause G, Menzel M, Pienkny S, Kiesow A, Deising HB, Wirsel SGR. Two genes in a pathogenicity gene cluster encoding secreted proteins are required for appressorial penetration and infection of the maize anthracnose fungus Colletotrichum graminicola. Environ Microbiol 2019; 21:4773-4791. [PMID: 31599055 DOI: 10.1111/1462-2920.14819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 01/14/2023]
Abstract
To avoid pathogen-associated molecular pattern recognition, the hemibiotrophic maize pathogen Colletotrichum graminicola secretes proteins mediating the establishment of biotrophy. Targeted deletion of 26 individual candidate genes and seven gene clusters comprising 32 genes of C. graminicola identified a pathogenicity cluster (CLU5) of five co-linear genes, all of which, with the exception of CLU5b, encode secreted proteins. Targeted deletion of all genes of CLU5 revealed that CLU5a and CLU5d are required for full appressorial penetration competence, with virulence deficiencies independent of the host genotype and organ inoculated. Cytorrhysis experiments and microscopy showed that Δclu5a mutants form pressurized appressoria, but they are hampered in forming penetration pores and fail to differentiate a penetration peg. Whereas Δclu5d mutants elicited WT-like papillae, albeit at increased frequencies, papillae induced by Δclu5a mutants were much smaller than those elicited by the WT. Synteny of CLU5 is not only conserved in Colletotrichum spp. but also in additional species of Sordariomycetes including insect pathogens and saprophytes suggesting importance of CLU5 for fungal biology. Since CLU5a and CLU5d also occur in non-pathogenic fungi and since they are expressed prior to plant invasion and even in vegetative hyphae, the encoded proteins probably do not act primarily as effectors.
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Affiliation(s)
- Iris Eisermann
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Fabian Weihmann
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Jorrit-Jan Krijger
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Christian Kröling
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany.,Sächsisches Landesamt für Umwelt, Landwirtschaft und Geologie, Abteilung Obst-, Gemüse- und Weinbau, August-Böckstiegel-Str. 1, D-01326, Dresden-Pillnitz, Germany
| | - Gerd Hause
- Biozentrum der Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 22, D-06120, Halle (Saale), Germany
| | - Matthias Menzel
- Fraunhofer-Institut für Mikrostruktur von Werkstoffen und Systemen, Biologische und makromolekulare Materialien, Walter-Hülse-Str. 1, D-06120, Halle (Saale), Germany
| | - Silke Pienkny
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Andreas Kiesow
- Fraunhofer-Institut für Mikrostruktur von Werkstoffen und Systemen, Biologische und makromolekulare Materialien, Walter-Hülse-Str. 1, D-06120, Halle (Saale), Germany
| | - Holger B Deising
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Stefan G R Wirsel
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
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31
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Oshiquiri LH, Dos Santos KRA, Ferreira Junior SA, Steindorff AS, Barbosa Filho JR, Mota TM, Ulhoa CJ, Georg RC. Trichoderma harzianum transcriptome in response to cadmium exposure. Fungal Genet Biol 2019; 134:103281. [PMID: 31626987 DOI: 10.1016/j.fgb.2019.103281] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 11/18/2022]
Abstract
Cadmium (Cd) is a heavy metal present in the environment mainly as a result of industrial contamination that can cause toxic effects to life. Some microorganisms, as Trichoderma harzianum, a fungus used in biocontrol, are able to survive in polluted environments and act as bioremediators. Aspects about the tolerance to the metal have been widely studied in other fungi although there are a few reports about the response of T. harzianum. In this study, we determined the effects of cadmium over growth of T. harzianum and used RNA-Seq to identify significant genes and processes regulated in the metal presence. Cadmium inhibited the fungus growth proportionally to its concentration although the fungus exhibited tolerance as it continued to grow, even in the highest concentrations used. A total of 3767 (1993 up and 1774 down) and 2986 (1606 up and 1380 down) differentially expressed genes were detected in the mycelium of T. harzianum cultivated in the presence of 1.0 mg mL-1 or 2.0 mg mL-1 of CdCl2, respectively, compared to the absence of the metal. Of these, 2562 were common to both treatments. Biological processes related to cellular homeostasis, transcription initiation, sulfur compound biosynthetic and metabolic processes, RNA processing, protein modification and vesicle-mediated transport were up-regulated. Carbohydrate metabolic processes were down-regulated. Pathway enrichment analysis indicated induction of glutathione and its precursor's metabolism. Interestingly, it also indicated an intense transcriptional induction, especially by up-regulation of spliceosome components. Carbohydrate metabolism was repressed, especially the mycoparasitism-related genes, suggesting that the mycoparasitic ability of T. harzianum could be affected during cadmium exposure. These results contribute to the advance of the current knowledge about the response of T. harzianum to cadmium exposure and provide significant targets for biotechnological improvement of this fungus as a bioremediator and a biocontrol agent.
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Affiliation(s)
- Letícia Harumi Oshiquiri
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil
| | | | | | - Andrei Stecca Steindorff
- U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | | | - Thuana Marcolino Mota
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil
| | - Cirano José Ulhoa
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil
| | - Raphaela Castro Georg
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás CEP:74690-900, Brazil.
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Hsp genes are differentially expressed during Trichoderma asperellum self-recognition, mycoparasitism and thermal stress. Microbiol Res 2019; 227:126296. [DOI: 10.1016/j.micres.2019.126296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 06/04/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
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Ji S, Liu Z, Liu B, Wang Y. Comparative analysis of biocontrol agent Trichoderma asperellum ACCC30536 transcriptome during its interaction with Populus davidiana × P. alba var. pyramidalis. Microbiol Res 2019; 227:126294. [PMID: 31421718 DOI: 10.1016/j.micres.2019.126294] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 12/11/2022]
Abstract
After exposure to with Populus davidiana × P. alba var. pyramidalis, the expression of genes in Trichoderma asperellum were compared in four transcriptomes. The top 20 high expression genes included six heat shock proteins and three hydrophobins, indicating that Trichoderma can rapidly adapt to environment stresses and elicit a plant defense response. The genes, involved in the interaction between Trichoderma and plant, showed an increasing expression level, for example sugar transporters, EPL1s, endoxylanases, pectin lyases, and nitrilases. Interestingly, sugar transporters also showed high expression when T. asperellum was cultured on medium lacking a carbon substrate, which would contribute to T. asperellum's survival and domination in ecological niche competition. And the genes related to mycoparasitism were expressed abundantly following T. asperellum's interaction with PdPap, indicating the PdPap induction could enhance the mycoparasitic ability of T. asperellum. Twelve chitinases and five glucanases showed higher expression in transcriptome Cs, indicating that T. asperellum secretes both types of enzyme before interacting with pathogens, allowing T. asperellum to implement mycoparasitism and obtain more energy. Many novel transcripts were obtained in each transcriptome, which may play important roles in the biocontrol process of T. asperellum. Interestingly, T. asperellum undergo constitutive alternative splicing in the biocontrol process: Seven biocontrol genes were alternative spliced via intron retention. qRT-PCR analysis proved that intron retention is negatively associated with the expression of chitinase, oligopeptide transporters, and beta-lactamase. However, the percentage of MAPK intron retention was quite low, suggesting that intron retention has little effect on the function of MAPK.
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Affiliation(s)
- Shida Ji
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Zhihua Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China
| | - Bin Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China
| | - Yucheng Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China.
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Gilbert KB, Holcomb EE, Allscheid RL, Carrington JC. Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes. PLoS One 2019; 14:e0219207. [PMID: 31339899 PMCID: PMC6655640 DOI: 10.1371/journal.pone.0219207] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/18/2019] [Indexed: 11/25/2022] Open
Abstract
The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 88% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.
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Affiliation(s)
- Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Emily E. Holcomb
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Robyn L. Allscheid
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - James C. Carrington
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
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Silva RN, Monteiro VN, Steindorff AS, Gomes EV, Noronha EF, Ulhoa CJ. Trichoderma/pathogen/plant interaction in pre-harvest food security. Fungal Biol 2019; 123:565-583. [PMID: 31345411 DOI: 10.1016/j.funbio.2019.06.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 01/17/2023]
Abstract
Large losses before crop harvesting are caused by plant pathogens, such as viruses, bacteria, oomycetes, fungi, and nematodes. Among these, fungi are the major cause of losses in agriculture worldwide. Plant pathogens are still controlled through application of agrochemicals, causing human disease and impacting environmental and food security. Biological control provides a safe alternative for the control of fungal plant pathogens, because of the ability of biocontrol agents to establish in the ecosystem. Some Trichoderma spp. are considered potential agents in the control of fungal plant diseases. They can interact directly with roots, increasing plant growth, resistance to diseases, and tolerance to abiotic stress. Furthermore, Trichoderma can directly kill fungal plant pathogens by antibiosis, as well as via mycoparasitism strategies. In this review, we will discuss the interactions between Trichoderma/fungal pathogens/plants during the pre-harvest of crops. In addition, we will highlight how these interactions can influence crop production and food security. Finally, we will describe the future of crop production using antimicrobial peptides, plants carrying pathogen-derived resistance, and plantibodies.
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Affiliation(s)
- Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
| | - Valdirene Neves Monteiro
- Campus of Exact Sciences and Technologies, Campus Henrique Santillo, Anapolis, Goiás State, Brazil
| | - Andrei Stecca Steindorff
- U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Eriston Vieira Gomes
- Department of Biofunctional, Center of Higher Education Morgana Potrich Eireli, Morgana Potrich College, Mineiros, Goiás, Brazil
| | | | - Cirano J Ulhoa
- Department of Biochemistry and Cellular Biology, Biological Sciences Institute, Campus Samambaia, Federal University of Goiás (UFG), Goiânia, Goiás, Brazil
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36
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Kubicek CP, Steindorff AS, Chenthamara K, Manganiello G, Henrissat B, Zhang J, Cai F, Kopchinskiy AG, Kubicek EM, Kuo A, Baroncelli R, Sarrocco S, Noronha EF, Vannacci G, Shen Q, Grigoriev IV, Druzhinina IS. Evolution and comparative genomics of the most common Trichoderma species. BMC Genomics 2019; 20:485. [PMID: 31189469 PMCID: PMC6560777 DOI: 10.1186/s12864-019-5680-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/09/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood. RESULTS We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. CONCLUSIONS Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist.
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Affiliation(s)
- Christian P Kubicek
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- , Vienna, Austria
| | - Andrei S Steindorff
- Departamento de Biologia Celular, Universidade de Brasília, Brasíla, DF, Brazil
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Komal Chenthamara
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Gelsomina Manganiello
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", Naples, Portici, Italy
| | - Bernard Henrissat
- CNRS, Aix-Marseille Université, Marseille, France
- INRA, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jian Zhang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Feng Cai
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Alexey G Kopchinskiy
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | | | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Riccardo Baroncelli
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Campus de Villamayor, Calle Del Duero, Villamayor, España
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | | | - Giovanni Vannacci
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Campus de Villamayor, Calle Del Duero, Villamayor, España
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
| | - Irina S Druzhinina
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria.
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
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Morán-Diez ME, Carrero-Carrón I, Rubio MB, Jiménez-Díaz RM, Monte E, Hermosa R. Transcriptomic Analysis of Trichoderma atroviride Overgrowing Plant-Wilting Verticillium dahliae Reveals the Role of a New M14 Metallocarboxypeptidase CPA1 in Biocontrol. Front Microbiol 2019; 10:1120. [PMID: 31191472 PMCID: PMC6545926 DOI: 10.3389/fmicb.2019.01120] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/03/2019] [Indexed: 11/25/2022] Open
Abstract
Verticillium dahliae, a vascular-colonizing fungus, causes economically important wilt diseases in many crops, including olive trees. Trichoderma spp. have demonstrated an effective contribution as biocontrol agents against this pathogen through a variety of mechanisms that may involve direct mycoparasitism and antibiosis. However, molecular aspects underlaying Trichoderma–V. dahliae interactions are not well known yet due to the few studies in which this pathogen has been used as a target for Trichoderma. In the present study, Trichoderma atroviride T11 overgrew colonies of V. dahliae on agar plates and inhibited growth of highly virulent defoliating (D) V. dahliae V-138I through diffusible molecules and volatile organic compounds produced before contact. A Trichoderma microarray approach of T11 growing alone (CON), and before contact (NV) or overgrowing (OV) colonies of V-138I, helped to identify 143 genes that differed significantly in their expression level by more than twofold between OV and CON or NV. Functional annotation of these genes indicated a marked up-regulation of hydrolytic, catalytic and transporter activities, and secondary metabolic processes when T11 overgrew V-138I. This transcriptomic analysis identified peptidases as enzymatic activity overrepresented in the OV condition, and the cpa1 gene encoding a putative carboxypeptidase (ID number 301733) was selected to validate this study. The role of cpa1 in strain T11 on antagonism of V-138I was analyzed by a cpa1-overexpression approach. The increased levels of cpa1 expression and protease activity in the cpa1-overexpressed transformants compared to those in wild-type or transformation control strains were followed by significantly higher antifungal activity against V-138I in in vitro assays. The use of Trichoderma spp. for the integrated management of plant diseases caused by V. dahliae requires a better understanding of the molecular mechanisms underlying this interaction that might provide an increase on its efficiency.
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Affiliation(s)
- María E Morán-Diez
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Irene Carrero-Carrón
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain.,College of Agriculture and Forestry (ETSIAM), University of Córdoba, Córdoba, Spain
| | - M Belén Rubio
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Rafael M Jiménez-Díaz
- College of Agriculture and Forestry (ETSIAM), University of Córdoba, Córdoba, Spain.,Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Córdoba, Spain
| | - Enrique Monte
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Rosa Hermosa
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
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Zhang J, Miao Y, Rahimi MJ, Zhu H, Steindorff A, Schiessler S, Cai F, Pang G, Chenthamara K, Xu Y, Kubicek CP, Shen Q, Druzhinina IS. Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi. Environ Microbiol 2019; 21:2644-2658. [PMID: 30815928 PMCID: PMC6850483 DOI: 10.1111/1462-2920.14575] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 12/01/2022]
Abstract
When resources are limited, the hypocrealean fungus Trichoderma guizhouense can overgrow another hypocrealean fungus Fusarium oxysporum, cause sporadic cell death and arrest growth. A transcriptomic analysis of this interaction shows that T. guizhouense undergoes a succession of metabolic stresses while F. oxysporum responded relatively neutrally but used the constitutive expression of several toxin‐encoding genes as a protective strategy. Because of these toxins, T. guizhouense cannot approach it is potential host on the substrate surface and attacks F. oxysporum from above. The success of T. guizhouense is secured by the excessive production of hydrogen peroxide (H2O2), which is stored in microscopic bag‐like guttation droplets hanging on the contacting hyphae. The deletion of NADPH oxidase nox1 and its regulator, nor1 in T. guizhouense led to a substantial decrease in H2O2 formation with concomitant loss of antagonistic activity. We envision the role of NOX proteins in the antagonism of T. guizhouense as an example of metabolic exaptation evolved in this fungus because the primary function of these ancient proteins was probably not linked to interfungal relationships. In support of this, F. oxysporum showed almost no transcriptional response to T. guizhouense Δnox1 strain indicating the role of NOX/H2O2 in signalling and fungal communication.
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Affiliation(s)
- Jian Zhang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Mohammad Javad Rahimi
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Hong Zhu
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Andrei Steindorff
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Sabine Schiessler
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Feng Cai
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Guan Pang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Komal Chenthamara
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Yu Xu
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Christian P Kubicek
- Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria.,Steinschoetelgasse 7,1100, Vienna, Austria
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Irina S Druzhinina
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Microbiology and Applied Genomics Group, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
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Whole RNA-sequencing and gene expression analysis of Trichoderma harzianum Tr-92 under chlamydospore-producing condition. Genes Genomics 2019; 41:689-699. [PMID: 30968334 DOI: 10.1007/s13258-019-00812-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/21/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Trichoderma is one of the most important biocontrol fungi, which could produce mycelia, conidiospores, and chlamydospores three types of propagules under different conditions. Chlamydospores are produced in harsh conditions in various fungi, and may be more resistant to adverse conditions. However, the knowledge associated with the mechanism of chlamydospore formation remained unclear in Trichoderma. OBJECTIVES This study is aimed to explore the essential genes and regulatory pathways associated with chlamydospore formation in Trichoderma. METHODS The culture condition, survival rate, and biocontrol effects of chlamydospores and conidiospores from Trichoderma.harzianum Tr-92 were determined. Furthermore, the whole transcriptome profiles of T. harzianum Tr-92 under chlamydospore-producing and chlamydospore-nonproducing conditions were performed. RESULTS T. harzianum Tr-92 produced chlamydospores under particular conditions, and chlamydospore-based formulation of T. harzianum Tr-92 exhibited higher biocontrol ability against Botrytis cinerea in cucumber than conidoiospore-based formulation. In the transcriptome analysis, a total of 2,029 differentially expressed genes (DEGs) were identified in T. harzianum Tr-92 under chlamydospore-producing condition, compared to that under chlamydospore-nonproducing condition. GO classification indicated that the DEGs were significantly enriched in 284 terms among biological process, cellular components and molecular function categories. A total of 19 pathways were observed with DEGs by KEGG analysis. Furthermore, fifteen DEGs were verified by quantitative real-time PCR, and the expression profiles were consistent with the transcriptome data. CONCLUSION The results would provide a basis on the molecular mechanisms underlying Trichoderma sporulation, which would assist the development and application of fungal biocontrol agents.
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Iqbal M, Dubey M, Gudmundsson M, Viketoft M, Jensen DF, Karlsson M. Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea. BMC Evol Biol 2018; 18:171. [PMID: 30445903 PMCID: PMC6240243 DOI: 10.1186/s12862-018-1291-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 11/06/2018] [Indexed: 11/18/2022] Open
Abstract
Background The ascomycete fungus Clonostachys rosea (order Hypocreales) can control several important plant diseases caused by plant pathogenic fungi and nematodes. Subtilisin-like serine proteases are considered to play an important role in pathogenesis in entomopathogenic, mycoparasitic, and nematophagous fungi used for biological control. In this study, we analysed the evolutionary histories of protease gene families, and investigated sequence divergence and regulation of serine protease genes in C. rosea. Results Proteases of selected hypocrealean fungal species were classified into families based on the MEROPS peptidase database. The highest number of protease genes (590) was found in Fusarium solani, followed by C. rosea with 576 genes. Analysis of gene family evolution identified non-random changes in gene copy numbers in the five serine protease gene families S1A, S8A, S9X, S12 and S33. Four families, S1A, S8A, S9X, and S33, displayed gene gains in C. rosea. A gene-tree / species-tree reconciliation analysis of the S8A family revealed that the gene copy number increase in C. rosea was primarily associated with the S08.054 (proteinase K) subgroup. In addition, regulatory and predicted structural differences, including twelve sites evolving under positive selection, among eighteen C. rosea S8A serine protease paralog genes were also observed. The C. rosea S8A serine protease gene prs6 was induced during interaction with the plant pathogenic species F. graminearum. Conclusions Non-random increases in S8A, S9X and S33 serine protease gene numbers in the mycoparasitic species C. rosea, Trichoderma atroviride and T. virens suggests an involvement in fungal-fungal interactions. Regulatory and predicted structural differences between C. rosea S8A paralogs indicate that functional diversification is driving the observed increase in gene copy numbers. The induction of prs6 expression in C. rosea during confrontation with F. graminearum suggests an involvement of the corresponding protease in fungal-fungal interactions. The results pinpoint the importance of serine proteases for ecological niche adaptation in C. rosea, including a potential role in the mycoparasitic attack on fungal prey. Electronic supplementary material The online version of this article (10.1186/s12862-018-1291-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mudassir Iqbal
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden
| | - Maria Viketoft
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, SE-75007, Uppsala, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden
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41
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Kredics L, Chen L, Kedves O, Büchner R, Hatvani L, Allaga H, Nagy VD, Khaled JM, Alharbi NS, Vágvölgyi C. Molecular Tools for Monitoring Trichoderma in Agricultural Environments. Front Microbiol 2018; 9:1599. [PMID: 30090089 PMCID: PMC6068273 DOI: 10.3389/fmicb.2018.01599] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Abstract
Various Trichoderma species possess significance in agricultural systems as biofertilizers or biocontrol agents (BCAs). Besides these beneficial features, certain Trichoderma species can also act as agricultural pests, causing the green mold disease of cultivated mushrooms. This double-faced nature of the genus in agricultural environments points at the importance of proper monitoring tools, which can be used to follow the presence and performance of candidate as well as patented and/or registered biocontrol strains, to assess the possible risks arising from their application, but also to track harmful, unwanted Trichoderma species like the green molds in mushroom growing facilities. The objective of this review is to discuss the molecular tools available for the species- and strain-specific monitoring of Trichoderma, ranging from immunological approaches and fingerprinting tools to exogenous markers, specific primers used in polymerase chain reaction (PCR) as well as "omics" approaches.
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Affiliation(s)
- László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Liqiong Chen
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Orsolya Kedves
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Rita Büchner
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Lóránt Hatvani
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Henrietta Allaga
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Viktor D Nagy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Jamal M Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Naiyf S Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.,Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Nygren K, Dubey M, Zapparata A, Iqbal M, Tzelepis GD, Durling MB, Jensen DF, Karlsson M. The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey. Evol Appl 2018; 11:931-949. [PMID: 29928301 PMCID: PMC5999205 DOI: 10.1111/eva.12609] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/26/2018] [Indexed: 01/31/2023] Open
Abstract
Clonostachys rosea is a necrotrophic mycoparasitic fungus, used for biological control of plant pathogenic fungi. A better understanding of the underlying mechanisms resulting in successful biocontrol is important for knowledge-based improvements of the application and use of biocontrol in agricultural production systems. Transcriptomic analyses revealed that C. rosea responded with both common and specific gene expression during interactions with the fungal prey species Botrytis cinerea and Fusarium graminearum. Genes predicted to encode proteins involved in membrane transport, biosynthesis of secondary metabolites and carbohydrate-active enzymes were induced during the mycoparasitic attack. Predicted major facilitator superfamily (MFS) transporters constituted 54% of the induced genes, and detailed phylogenetic and evolutionary analyses showed that a majority of these genes belonged to MFS gene families evolving under selection for increased paralog numbers, with predicted functions in drug resistance and transport of carbohydrates and small organic compounds. Sequence analysis of MFS transporters from family 2.A.1.3.65 identified rapidly evolving loop regions forming the entry to the transport tunnel, indicating changes in substrate specificity as a target for selection. Deletion of the MFS transporter gene mfs464 resulted in mutants with increased growth inhibitory activity against F. graminearum, providing evidence for a function in interspecific fungal interactions. In summary, we show that the mycoparasite C. rosea can distinguish between fungal prey species and modulate its transcriptomic responses accordingly. Gene expression data emphasize the importance of secondary metabolites in mycoparasitic interactions.
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Affiliation(s)
- Kristiina Nygren
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Antonio Zapparata
- Department of Agriculture, Food and EnvironmentUniversity of PisaPisaItaly
| | - Mudassir Iqbal
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Georgios D. Tzelepis
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
- Department of Plant BiologyUppsala BiocenterLinnean Centre for Plant BiologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
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Biochemical and Molecular Study of Trichoderma harzianum Enriched Secretome Protein Profiles Using Lectin Affinity Chromatography. Appl Biochem Biotechnol 2018; 187:1-13. [DOI: 10.1007/s12010-018-2795-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/24/2018] [Indexed: 01/16/2023]
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MIP diversity from Trichoderma: Structural considerations and transcriptional modulation during mycoparasitic association with Fusarium solani olive trees. PLoS One 2018; 13:e0193760. [PMID: 29543834 PMCID: PMC5854309 DOI: 10.1371/journal.pone.0193760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 02/17/2018] [Indexed: 11/19/2022] Open
Abstract
Major intrinsic proteins (MIP) are characterized by a transmembrane pore-type architecture that facilitates transport across biomembranes of water and a variety of low molecular weight solutes. They are found in all parts of life, with remarkable protein diversity. Very little is known about MIP from fungi. And yet, it can legitimately be stated that MIP are pivotal molecular components in the privileged relationships fungi enjoy with plants or soil fauna in various environments. To date, MIP have never been studied in a mycoparasitism situation. In this study, the diversity, expression and functional prediction of MIP from the genus Trichoderma were investigated. Trichoderma spp. genomes have at least seven aquaporin genes. Based on a phylogenetic analysis of the translated sequences, members were assigned to the AQP, AQGP and XIP subfamilies. In in vitro and in planta assays with T. harzianum strain Ths97, expression analyses showed that four genes were constitutively expressed. In a mycoparasitic context with Fusarium solani, the causative agent of fusarium dieback on olive tree roots, these genes were up-regulated. This response is of particular interest in analyzing the MIP promoter cis-regulatory motifs, most of which are involved in various carbon and nitrogen metabolisms. Structural analyses provide new insights into the possible role of structural checkpoints by which these members transport water, H2O2, glycerol and, more generally, linear polyols across the membranes. Taken together, these results provide the first evidence that MIP may play a key role in Trichoderma mycoparasitism lifestyle.
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Rodenburg SYA, Terhem RB, Veloso J, Stassen JHM, van Kan JAL. Functional Analysis of Mating Type Genes and Transcriptome Analysis during Fruiting Body Development of Botrytis cinerea. mBio 2018; 9:e01939-17. [PMID: 29440571 PMCID: PMC5821092 DOI: 10.1128/mbio.01939-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/17/2018] [Indexed: 02/07/2023] Open
Abstract
Botrytis cinerea is a plant-pathogenic fungus producing apothecia as sexual fruiting bodies. To study the function of mating type (MAT) genes, single-gene deletion mutants were generated in both genes of the MAT1-1 locus and both genes of the MAT1-2 locus. Deletion mutants in two MAT genes were entirely sterile, while mutants in the other two MAT genes were able to develop stipes but never formed an apothecial disk. Little was known about the reprogramming of gene expression during apothecium development. We analyzed transcriptomes of sclerotia, three stages of apothecium development (primordia, stipes, and apothecial disks), and ascospores by RNA sequencing. Ten secondary metabolite gene clusters were upregulated at the onset of sexual development and downregulated in ascospores released from apothecia. Notably, more than 3,900 genes were differentially expressed in ascospores compared to mature apothecial disks. Among the genes that were upregulated in ascospores were numerous genes encoding virulence factors, which reveals that ascospores are transcriptionally primed for infection prior to their arrival on a host plant. Strikingly, the massive transcriptional changes at the initiation and completion of the sexual cycle often affected clusters of genes, rather than randomly dispersed genes. Thirty-five clusters of genes were jointly upregulated during the onset of sexual reproduction, while 99 clusters of genes (comprising >900 genes) were jointly downregulated in ascospores. These transcriptional changes coincided with changes in expression of genes encoding enzymes participating in chromatin organization, hinting at the occurrence of massive epigenetic regulation of gene expression during sexual reproduction.IMPORTANCE Fungal fruiting bodies are formed by sexual reproduction. We studied the development of fruiting bodies ("apothecia") of the ubiquitous plant-pathogenic ascomycete Botrytis cinerea The role of mating type genes in apothecium development was investigated by targeted mutation. Two genes are essential for the initiation of sexual development; mutants in these genes are sterile. Two other genes were not essential for development of stipes; however, they were essential for stipes to develop a disk and produce sexual ascospores. We examined gene expression profiles during apothecium development, as well as in ascospores sampled from apothecia. We provide the first study ever of the transcriptome of pure ascospores in a filamentous fungus. The expression of numerous genes involved in plant infection was induced in the ascospores, implying that ascospores are developmentally primed for infection before their release from apothecia.
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Affiliation(s)
- Sander Y A Rodenburg
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Wageningen University, Bioinformatics Group, Wageningen, The Netherlands
| | - Razak B Terhem
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Javier Veloso
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Department of Plant Physiology, Faculty of Sciences, University of A Coruña, A Coruña, Spain
| | - Joost H M Stassen
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
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Hu X, Qin L, Roberts DP, Lakshman DK, Gong Y, Maul JE, Xie L, Yu C, Li Y, Hu L, Liao X, Liao X. Characterization of mechanisms underlying degradation of sclerotia of Sclerotinia sclerotiorum by Aspergillus aculeatus Asp-4 using a combined qRT-PCR and proteomic approach. BMC Genomics 2017; 18:674. [PMID: 28859614 PMCID: PMC5580281 DOI: 10.1186/s12864-017-4016-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background The biological control agent Aspergillus aculeatus Asp-4 colonizes and degrades sclerotia of Sclerotinia sclerotiorum resulting in reduced germination and disease caused by this important plant pathogen. Molecular mechanisms of mycoparasites underlying colonization, degradation, and reduction of germination of sclerotia of this and other important plant pathogens remain poorly understood. Results An RNA-Seq screen of Asp-4 growing on autoclaved, ground sclerotia of S. sclerotiorum for 48 h identified 997 up-regulated and 777 down-regulated genes relative to this mycoparasite growing on potato dextrose agar (PDA) for 48 h. qRT-PCR time course experiments characterized expression dynamics of select genes encoding enzymes functioning in degradation of sclerotial components and management of environmental conditions, including environmental stress. This analysis suggested co-temporal up-regulation of genes functioning in these two processes. Proteomic analysis of Asp-4 growing on this sclerotial material for 48 h identified 26 up-regulated and 6 down-regulated proteins relative to the PDA control. Certain proteins with increased abundance had putative functions in degradation of polymeric components of sclerotia and the mitigation of environmental stress. Conclusions Our results suggest co-temporal up-regulation of genes involved in degradation of sclerotial compounds and mitigation of environmental stress. This study furthers the analysis of mycoparasitism of sclerotial pathogens by providing the basis for molecular characterization of a previously uncharacterized mycoparasite-sclerotial interaction. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4016-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaojia Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Lu Qin
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Daniel P Roberts
- Sustainable Agricultural Systems Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, USDA-Agricultural Research Service, Beltsville, MD, 20705-2350, USA.
| | - Dilip K Lakshman
- Sustainable Agricultural Systems Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, USDA-Agricultural Research Service, Beltsville, MD, 20705-2350, USA
| | - Yangmin Gong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Jude E Maul
- Sustainable Agricultural Systems Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, USDA-Agricultural Research Service, Beltsville, MD, 20705-2350, USA
| | - Lihua Xie
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Changbing Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Yinshui Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Lei Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Xiangsheng Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Xing Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China.
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Sharma V, Salwan R, Sharma PN, Gulati A. Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects of Trichoderma. Front Microbiol 2017; 8:1602. [PMID: 28900417 PMCID: PMC5581810 DOI: 10.3389/fmicb.2017.01602] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022] Open
Abstract
Genome-wide studies of transcripts expression help in systematic monitoring of genes and allow targeting of candidate genes for future research. In contrast to relatively stable genomic data, the expression of genes is dynamic and regulated both at time and space level at different level in. The variation in the rate of translation is specific for each protein. Both the inherent nature of an mRNA molecule to be translated and the external environmental stimuli can affect the efficiency of the translation process. In biocontrol agents (BCAs), the molecular response at translational level may represents noise-like response of absolute transcript level and an adaptive response to physiological and pathological situations representing subset of mRNAs population actively translated in a cell. The molecular responses of biocontrol are complex and involve multistage regulation of number of genes. The use of high-throughput techniques has led to rapid increase in volume of transcriptomics data of Trichoderma. In general, almost half of the variations of transcriptome and protein level are due to translational control. Thus, studies are required to integrate raw information from different “omics” approaches for accurate depiction of translational response of BCAs in interaction with plants and plant pathogens. The studies on translational status of only active mRNAs bridging with proteome data will help in accurate characterization of only a subset of mRNAs actively engaged in translation. This review highlights the associated bottlenecks and use of state-of-the-art procedures in addressing the gap to accelerate future accomplishment of biocontrol mechanisms.
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Affiliation(s)
- Vivek Sharma
- Department of Plant Pathology, Choudhary Sarwan Kumar Himachal Pradesh Agricultural UniversityPalampur, India
| | - Richa Salwan
- Department of Veterinary Microbiology, Choudhary Sarwan Kumar Himachal Pradesh Agricultural UniversityPalampur, India
| | - P N Sharma
- Department of Plant Pathology, Choudhary Sarwan Kumar Himachal Pradesh Agricultural UniversityPalampur, India
| | - Arvind Gulati
- Institute of Himalayan Bioresource TechnologyPalampur, India
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Saravanakumar K, Li Y, Yu C, Wang QQ, Wang M, Sun J, Gao JX, Chen J. Effect of Trichoderma harzianum on maize rhizosphere microbiome and biocontrol of Fusarium Stalk rot. Sci Rep 2017; 7:1771. [PMID: 28496167 PMCID: PMC5431858 DOI: 10.1038/s41598-017-01680-w] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/30/2017] [Indexed: 01/23/2023] Open
Abstract
Fusarium stalk rot (FSR) caused by Fusarium graminearum (FG) significantly affects the productivity of maize grain crops. Application of agrochemicals to control the disease is harmful to environment. In this regard, use of biocontrol agent (BCA) is an alternative to agrochemicals. Although Trichoderma species are known as BCA, the selection of host-pathogen specific Trichoderma is essential for the successful field application. Hence, we screened a total of 100 Trichoderma isolates against FG, selected Trichoderma harzianum (CCTCC-RW0024) for greenhouse experiments and studied its effect on changes of maize rhizosphere microbiome and biocontrol of FSR. The strain CCTCC-RW0024 displayed high antagonistic activity (96.30%), disease reduction (86.66%), biocontrol-related enzyme and gene expression. The root colonization of the strain was confirmed by eGFP tagging and qRT-PCR analysis. Pyrosequencing revealed that exogenous inoculation of the strain in maize rhizosphere increased the plant growth promoting acidobacteria (18.4%), decreased 66% of FG, and also increased the plant growth. In addition, metabolites of this strain could interact with pathogenicity related transcriptional cofactor FgSWi6, thereby contributing to its inhibition. It is concluded that T. harzianum strain CCTCC-RW0024 is a potential BCA against FSR.
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Affiliation(s)
- Kandasamy Saravanakumar
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Yaqian Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China.
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China.
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China.
| | - Chuanjin Yu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Qiang-Qiang Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Meng Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Jianan Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Jin-Xin Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China.
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China.
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China.
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Identification of differentially expressed genes from Trichoderma atroviride strain SS003 in the presence of cell wall of Cronartium ribicola. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0512-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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50
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Shaw S, Le Cocq K, Paszkiewicz K, Moore K, Winsbury R, de Torres Zabala M, Studholme DJ, Salmon D, Thornton CR, Grant MR. Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil. MOLECULAR PLANT PATHOLOGY 2016; 17:1425-1441. [PMID: 27187266 PMCID: PMC6638342 DOI: 10.1111/mpp.12429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The free-living soil fungus Trichoderma hamatum strain GD12 is notable amongst Trichoderma strains in both controlling plant diseases and stimulating plant growth, a property enhanced during its antagonistic interactions with pathogens in soil. These attributes, alongside its markedly expanded genome and proteome compared with other biocontrol and plant growth-promoting Trichoderma strains, imply a rich potential for sustainable alternatives to synthetic pesticides and fertilizers for the control of plant disease and for increasing yields. The purpose of this study was to investigate the transcriptional responses of GD12 underpinning its biocontrol and plant growth promotion capabilities during antagonistic interactions with the pathogen Sclerotinia sclerotiorum in soil. Using an extensive mRNA-seq study capturing different time points during the pathogen-antagonist interaction in soil, we show that dynamic and biphasic signatures in the GD12 transcriptome underpin its biocontrol and plant (lettuce) growth-promoting activities. Functional predictions of differentially expressed genes demonstrate the enrichment of transcripts encoding proteins involved in transportation and oxidation-reduction reactions during both processes and an over-representation of siderophores. We identify a biphasic response during biocontrol characterized by a significant induction of transcripts encoding small-secreted cysteine-rich proteins, secondary metabolite-producing gene clusters and genes unique to GD12. These data support the hypothesis that Sclerotinia biocontrol is mediated by the synthesis and secretion of antifungal compounds and that GD12's unique reservoir of uncharacterized genes is actively recruited during the effective biological control of a plurivorous plant pathogen.
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Affiliation(s)
- Sophie Shaw
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
- Centre for Genome Enabled Biology and MedicineUniversity of Aberdeen23 St. Machar DriveOld AberdeenAB24 3RYUK
| | - Kate Le Cocq
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
- Sustainable Soils and Grassland Systems DepartmentRothamsted ResearchNorth WykeOkehamptonEX20 2SBUK
| | - Konrad Paszkiewicz
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - Karen Moore
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - Rebecca Winsbury
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Marta de Torres Zabala
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - David J. Studholme
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - Deborah Salmon
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - Christopher R. Thornton
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - Murray R. Grant
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
- School of Life Sciences, Gibbet Hill CampusUniversity of WarwickCoventryCV4 7ALUK
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