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Castañeda-Casasola CC, Nieto-Jacobo MF, Soares A, Padilla-Padilla EA, Anducho-Reyes MA, Brown C, Soth S, Esquivel-Naranjo EU, Hampton J, Mendoza-Mendoza A. Unveiling a Microexon Switch: Novel Regulation of the Activities of Sugar Assimilation and Plant-Cell-Wall-Degrading Xylanases and Cellulases by Xlr2 in Trichoderma virens. Int J Mol Sci 2024; 25:5172. [PMID: 38791210 DOI: 10.3390/ijms25105172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Functional microexons have not previously been described in filamentous fungi. Here, we describe a novel mechanism of transcriptional regulation in Trichoderma requiring the inclusion of a microexon from the Xlr2 gene. In low-glucose environments, a long mRNA including the microexon encodes a protein with a GAL4-like DNA-binding domain (Xlr2-α), whereas in high-glucose environments, a short mRNA that is produced encodes a protein lacking this DNA-binding domain (Xlr2-β). Interestingly, the protein isoforms differ in their impact on cellulase and xylanase activity. Deleting the Xlr2 gene reduced both xylanase and cellulase activity and growth on different carbon sources, such as carboxymethylcellulose, xylan, glucose, and arabinose. The overexpression of either Xlr2-α or Xlr2-β in T. virens showed that the short isoform (Xlr2-β) caused higher xylanase activity than the wild types or the long isoform (Xlr2-α). Conversely, cellulase activity did not increase when overexpressing Xlr2-β but was increased with the overexpression of Xlr2-α. This is the first report of a novel transcriptional regulation mechanism of plant-cell-wall-degrading enzyme activity in T. virens. This involves the differential expression of a microexon from a gene encoding a transcriptional regulator.
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Affiliation(s)
- Cynthia Coccet Castañeda-Casasola
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Centro Nacional de Referencia Fitosanitaria, Tecamac 55740, Mexico
| | | | - Amanda Soares
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Emir Alejandro Padilla-Padilla
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 04510, Mexico
| | - Miguel Angel Anducho-Reyes
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico
| | - Chris Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Sereyboth Soth
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Edgardo Ulises Esquivel-Naranjo
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Queretaro, Queretaro 76230, Mexico
| | - John Hampton
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
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Aamir M, Shanmugam V, Dubey MK, Husain FM, Adil M, Ansari WA, Rai A, Sah P. Transcriptomic characterization of Trichoderma harzianum T34 primed tomato plants: assessment of biocontrol agent induced host specific gene expression and plant growth promotion. BMC Plant Biol 2023; 23:552. [PMID: 37940862 PMCID: PMC10631224 DOI: 10.1186/s12870-023-04502-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 09/30/2023] [Indexed: 11/10/2023]
Abstract
In this study, we investigated the intricate interplay between Trichoderma and the tomato genome, focusing on the transcriptional and metabolic changes triggered during the late colonization event. Microarray probe set (GSE76332) was utilized to analyze the gene expression profiles changes of the un-inoculated control (tomato) and Trichoderma-tomato interactions for identification of the differentially expressed significant genes. Based on principal component analysis and R-based correlation, we observed a positive correlation between the two cross-comaparable groups, corroborating the existence of transcriptional responses in the host triggered by Trichoderma priming. The statistically significant genes based on different p-value cut-off scores [(padj-values or q-value); padj-value < 0.05], [(pcal-values); pcal-value < 0.05; pcal < 0.01; pcal < 0.001)] were cross compared. Through cross-comparison, we identified 156 common genes that were consistently significant across all probability thresholds, and showing a strong positive corelation between p-value and q-value in the selected probe sets. We reported TD2, CPT1, pectin synthase, EXT-3 (extensin-3), Lox C, and pyruvate kinase (PK), which exhibited upregulated expression, and Glb1 and nitrate reductase (nii), which demonstrated downregulated expression during Trichoderma-tomato interaction. In addition, microbial priming with Trichoderma resulted into differential expression of transcription factors related to systemic defense and flowering including MYB13, MYB78, ERF2, ERF3, ERF5, ERF-1B, NAC, MADS box, ZF3, ZAT10, A20/AN1, polyol sugar transporter like zinc finger proteins, and a novel plant defensin protein. The potential bottleneck and hub genes involved in this dynamic response were also identified. The protein-protein interaction (PPI) network analysis based on 25 topmost DEGS (pcal-value < 0.05) and the Weighted Correlation Gene Network Analysis (WGCNA) of the 1786 significant DEGs (pcal-value < 0.05) we reported the hits associated with carbohydrate metabolism, secondary metabolite biosynthesis, and the nitrogen metabolism. We conclude that the Trichoderma-induced microbial priming re-programmed the host genome for transcriptional response during the late colonization event and were characterized by metabolic shifting and biochemical changes specific to plant growth and development. The work also highlights the relevance of statistical parameters in understanding the gene regulatory dynamics and complex regulatory networks based on differential expression, co-expression, and protein interaction networks orchestrating the host responses to beneficial microbial interactions.
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Affiliation(s)
- Mohd Aamir
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi-110012, Delhi, India.
| | - V Shanmugam
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi-110012, Delhi, India
| | - Manish Kumar Dubey
- Department of Biotechnology, University Centre for Research & Development (UCRD), Chandigarh University, Punjab, 140413, India
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh-11451, Saudi Arabia
| | - Mohd Adil
- Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS, B2N2R9, Canada
| | - Waquar Akhter Ansari
- Department of Botany, Centre for Advanced Study, Institute of Science, Banaras Hindu University, Varanasi, 221002, India
| | - Ashutosh Rai
- Department of Basic and Social Sciences, College of Horticulture, Banda University of Agriculture and Technology, Uttar Pradesh, Banda, 210001, India
| | - Pankaj Sah
- Applied Sciences Department, College of Applied Sciences and Pharmacy, University of Technology and Applied Sciences-Muscat, Al Janubyyah Street, PO Box 74, Muscat, 133, Sultanate of Oman
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Tan B, Li Y, Deng D, Pan H, Zeng Y, Tan X, Zhuang W, Li Z. Rhizosphere inoculation of Nicotiana benthamiana with Trichoderma harzianum TRA1-16 in controlled environment agriculture: Effects of varying light intensities on the mutualism-parasitism interaction. Front Plant Sci 2022; 13:989155. [PMID: 36340354 PMCID: PMC9630631 DOI: 10.3389/fpls.2022.989155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Trichoderma spp., a genus of fast-growing and highly adaptable fungi that form symbiotic relationships with plant roots, rendering them ideal for practical use in controlled environment agriculture. Herein, this paper aims to understand how the Nicotiana benthamiana with inoculation of Trichoderma harzianum strain TRA1-16 responds to light intensity variation. Pot experiments were conducted under low and high light intensities (50 and 150 μmol·m-2·s-1, respectively) and microbial treatments. Plant growth, physio-biochemical attributes, activities of antioxidant enzymes, and phytohormones regulation were investigated. The results showed that for non-inoculated plants, the reduction in light intensity inhibited plant growth, nitrogen (N) and phosphorus (P) uptake, chlorophyll a/b, and carotenoid content. Trichoderma inoculation resulted in 1.17 to 1.51 times higher concentrations of available N and P in the soil than the non-inoculated group, with higher concentrations at high light intensity. Plant height, dry weight, nutrient uptake, and antioxidant activity were significantly increased after inoculation (p<0.05). However, the growth-promoting effect was less effective under low light conditions, with lower plant height and P content in plants. We suggested that when the light was attenuated, the mutualism of the Trichoderma turned into parasitism, slowing the growth of the host plant. The application of fungal inoculation techniques for plant growth promotion required coordination with appropriate light complementation. The mechanisms of coordination and interaction were proposed to be incorporated into the biological market theory.
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Affiliation(s)
- Bo Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, China
| | - Yihan Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, China
- Sichuan Development Guorun Water Investment Co. Ltd., Chengdu, China
| | | | - Hongli Pan
- Sichuan Academy of Forestry, Chengdu, China
| | - Yue Zeng
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, China
| | - Xiao Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, China
| | - Wenhua Zhuang
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, China
| | - Zhuo Li
- Key Laboratory of Water Saving Agriculture in Hill Areas in Southern China of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Rouina H, Tseng YH, Nataraja KN, Uma Shaanker R, Krüger T, Kniemeyer O, Brakhage A, Oelmüller R. Comparative Secretome Analyses of Trichoderma/Arabidopsis Co-cultures Identify Proteins for Salt Stress, Plant Growth Promotion, and Root Colonization. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.808430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Numerous Trichoderma strains are beneficial for plants, promote their growth, and confer stress tolerance. A recently described novel Trichoderma strain strongly promotes the growth of Arabidopsis thaliana seedlings on media with 50 mM NaCl, while 150 mM NaCl strongly stimulated root colonization and induced salt-stress tolerance in the host without growth promotion. To understand the dynamics of plant-fungus interaction, we examined the secretome from both sides and revealed a substantial change under different salt regimes, and during co-cultivation. Stress-related proteins, such as a fungal cysteine-rich Kp4 domain-containing protein which inhibits plant cell growth, fungal WSC- and CFEM-domain-containing proteins, the plant calreticulin, and cell-wall modifying enzymes, disappear when the two symbionts are co-cultured under high salt concentrations. In contrast, the number of lytic polysaccharide monooxygenases increases, which indicates that the fungus degrades more plant lignocellulose under salt stress and its lifestyle becomes more saprophytic. Several plant proteins involved in plant and fungal cell wall modifications and root colonization are only found in the co-cultures under salt stress, while the number of plant antioxidant proteins decreased. We identified symbiosis- and salt concentration-specific proteins for both partners. The Arabidopsis PYK10 and a fungal prenylcysteine lyase are only found in the co-culture which promoted plant growth. The comparative analysis of the secretomes supports antioxidant enzyme assays and suggests that both partners profit from the interaction under salt stress but have to invest more in balancing the symbiosis. We discuss the role of the identified stage- and symbiosis-specific fungal and plant proteins for salt stress, and conditions promoting root colonization and plant growth.
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Taylor JT, Wang KD, Horwitz B, Kolomiets M, Kenerley CM. Early Transcriptome Response of Trichoderma virens to Colonization of Maize Roots. Front Fungal Biol 2021; 2:718557. [PMID: 37744095 PMCID: PMC10512331 DOI: 10.3389/ffunb.2021.718557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/02/2021] [Indexed: 09/26/2023]
Abstract
Trichoderma virens is a well-known mycoparasitic fungal symbiont that is valued for its biocontrol capabilities. T. virens initiates a symbiotic relationship with a plant host through the colonization of its roots. To achieve colonization, the fungus must communicate with the host and evade its innate defenses. In this study, we explored the genes involved with the host communication and colonization process through transcriptomic profiling of the wild-type fungus and selected deletion mutants as they colonized maize roots. Transcriptome profiles of the T. virens colonization of maize roots over time revealed that 24 h post inoculation appeared to be a key time for plant-microbe communication, with many key gene categories, including signal transduction mechanisms and carbohydrate transport and metabolism, peaking in expression at this early colonization time point. The transcriptomic profiles of Sm1 and Sir1 deletion mutants in the presence of plants demonstrated that Sir1, rather than Sm1, appears to be the key regulator of the fungal response to maize, with 64% more unique differentially expressed genes compared to Sm1. Additionally, we developed a novel algorithm utilizing gene clustering and coexpression network analyses to select potential colonization-related gene targets for characterization. About 40% of the genes identified by the algorithm would have been missed using previous methods for selecting gene targets.
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Affiliation(s)
- James T. Taylor
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
| | - Ken-Der Wang
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
| | - Benjamin Horwitz
- Department of Biology, Technion Israel Institute of Technology, Haifa, Israel
| | - Michael Kolomiets
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
| | - Charles M. Kenerley
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Liu Q, Tang S, Meng X, Zhu H, Zhu Y, Liu D, Shen Q. Proteomic Analysis Demonstrates a Molecular Dialog Between Trichoderma guizhouense NJAU 4742 and Cucumber ( Cucumis sativus L.) Roots: Role in Promoting Plant Growth. Mol Plant Microbe Interact 2021; 34:631-644. [PMID: 33496609 DOI: 10.1094/mpmi-08-20-0240-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Trichoderma is a genus of filamentous fungi that play notable roles in stimulating plant growth after colonizing the root surface. However, the key proteins and molecular mechanisms governing this stimulation have not been completely elucidated. In this study, Trichoderma guizhouense NJAU 4742 was investigated in a hydroponic culture system after interacting with cucumber roots. The total proteins of the fungus were characterized, and the key metabolic pathways along with related genes were analyzed through proteomic and transcriptomic analyses. The roles played by the regulated proteins during the interaction between plants and NJAU 4742 were further examined. The intracellular or extracellular proteins from NJAU 4742 and extracellular proteins from cucumber were quantified, and the high-abundance proteins were determined which were primarily involved in the shikimate pathway (tryptophan, tyrosine, and phenylalanine metabolism, auxin biosynthesis, and secondary metabolite synthesis). Moreover, 15N-KNO3 labeling analysis indicated that NJAU 4742 had a strong ability to convert nitrogenous amino acids, nitrate, nitrile, and amines into ammonia. The auxin synthesis and ammonification metabolism pathways of NJAU 4742 significantly contributed to plant growth. The results of this study demonstrated the crucial metabolic pathways involved in the interactions between Trichoderma spp. and plants.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Qiumei Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Siyu Tang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Xiaohui Meng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Han Zhu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Yiyong Zhu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
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Schweiger R, Padilla-Arizmendi F, Nogueira-López G, Rostás M, Lawry R, Brown C, Hampton J, Steyaert JM, Müller C, Mendoza-Mendoza A. Insights into Metabolic Changes Caused by the Trichoderma virens-Maize Root Interaction. Mol Plant Microbe Interact 2021; 34:524-537. [PMID: 33166203 DOI: 10.1094/mpmi-04-20-0081-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The interactions of crops with root-colonizing endophytic microorganisms are highly relevant to agriculture, because endophytes can modify plant resistance to pests and increase crop yields. We investigated the interactions between the host plant Zea mays and the endophytic fungus Trichoderma virens at 5 days postinoculation grown in a hydroponic system. Wild-type T. virens and two knockout mutants, with deletion of the genes tv2og1 or vir4 involved in specialized metabolism, were analyzed. Root colonization by the fungal mutants was lower than that by the wild type. All fungal genotypes suppressed root biomass. Metabolic fingerprinting of roots, mycelia, and fungal culture supernatants was performed using ultrahigh performance liquid chromatography coupled to diode array detection and quadrupole time-of-flight tandem mass spectrometry. The metabolic composition of T. virens-colonized roots differed profoundly from that of noncolonized roots, with the effects depending on the fungal genotype. In particular, the concentrations of several metabolites derived from the shikimate pathway, including an amino acid and several flavonoids, were modulated. The expression levels of some genes coding for enzymes involved in these pathways were affected if roots were colonized by the ∆vir4 genotype of T. virens. Furthermore, mycelia and fungal culture supernatants of the different T. virens genotypes showed distinct metabolomes. Our study highlights the fact that colonization by endophytic T. virens leads to far-reaching metabolic changes, partly related to two fungal genes. Both metabolites produced by the fungus and plant metabolites modulated by the interaction probably contribute to these metabolic patterns. The metabolic changes in plant tissues may be interlinked with systemic endophyte effects often observed in later plant developmental stages.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Rabea Schweiger
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | | | | | - Michael Rostás
- Bio-Protection Research Centre, Lincoln University, Lincoln 7647, Canterbury, New Zealand
- Agricultural Entomology, Department of Crop Sciences, University of Göttingen, Grisebachstr. 6, 37077 Göttingen, Germany
| | - Robert Lawry
- Bio-Protection Research Centre, Lincoln University, Lincoln 7647, Canterbury, New Zealand
| | - Chris Brown
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - John Hampton
- Bio-Protection Research Centre, Lincoln University, Lincoln 7647, Canterbury, New Zealand
| | - Johanna M Steyaert
- Lincoln Agritech Ltd., PO Box 69133, Lincoln, Christchurch 7460, New Zealand
| | - Caroline Müller
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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Abbasi S, Sadeghi A, Omidvari M, Tahan V. The stimulators and responsive genes to induce systemic resistance against pathogens: An exclusive focus on tomato as a model plant. Biocatalysis and Agricultural Biotechnology 2021. [DOI: 10.1016/j.bcab.2021.101993] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Bashyal BM, Parmar P, Zaidi NW, Aggarwal R. Molecular Programming of Drought-Challenged Trichoderma harzianum-Bioprimed Rice ( Oryza sativa L.). Front Microbiol 2021; 12:655165. [PMID: 33927706 PMCID: PMC8076752 DOI: 10.3389/fmicb.2021.655165] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/24/2021] [Indexed: 12/18/2022] Open
Abstract
Trichoderma biopriming enhances rice growth in drought-stressed soils by triggering various plant metabolic pathways related to antioxidative defense, secondary metabolites, and hormonal upregulation. In the present study, transcriptomic analysis of rice cultivar IR64 bioprimed with Trichoderma harzianum under drought stress was carried out in comparison with drought-stressed samples using next-generation sequencing techniques. Out of the 2,506 significant (p < 0.05) differentially expressed genes (DEGs), 337 (15%) were exclusively expressed in drought-stressed plants, 382 (15%) were expressed in T. harzianum-treated drought-stressed plants, and 1,787 (70%) were commonly expressed. Furthermore, comparative analysis of upregulated and downregulated genes under stressed conditions showed that 1,053 genes (42%) were upregulated and 733 genes (29%) were downregulated in T. harzianum-treated drought-stressed rice plants. The genes exclusively expressed in T. harzianum-treated drought-stressed plants were mostly photosynthetic and antioxidative such as plastocyanin, small chain of Rubisco, PSI subunit Q, PSII subunit PSBY, osmoproteins, proline-rich protein, aquaporins, stress-enhanced proteins, and chaperonins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis states that the most enriched pathways were metabolic (38%) followed by pathways involved in the synthesis of secondary metabolites (25%), carbon metabolism (6%), phenyl propanoid (7%), and glutathione metabolism (3%). Some of the genes were selected for validation using real-time PCR which showed consistent expression as RNA-Seq data. Furthermore, to establish host-T. harzianum interaction, transcriptome analysis of Trichoderma was also carried out. The Gene Ontology (GO) analysis of T. harzianum transcriptome suggested that the annotated genes are functionally related to carbohydrate binding module, glycoside hydrolase, GMC oxidoreductase, and trehalase and were mainly upregulated, playing an important role in establishing the mycelia colonization of rice roots and its growth. Overall, it can be concluded that T. harzianum biopriming delays drought stress in rice cultivars by a multitude of molecular programming.
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Affiliation(s)
- Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Pooja Parmar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | | | - Rashmi Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
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12
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Ruangwong OU, Wonglom P, Suwannarach N, Kumla J, Thaochan N, Chomnunti P, Pitija K, Sunpapao A. Volatile Organic Compound from Trichoderma asperelloides TSU1: Impact on Plant Pathogenic Fungi. J Fungi (Basel) 2021; 7:187. [PMID: 33807949 DOI: 10.3390/jof7030187] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/28/2022] Open
Abstract
Soil microorganisms are well studied for their beneficial effects on plant growth and their impact on biocontrol agents. The production of volatile antifungal compounds emitted from soil fungi is considered to be an effective ability that can be applied in biofumigants in the control of plant diseases. A soil fungus, Trichoderma asperelloides TSU1, was isolated from flamingo flower cultivated soil and identified on the basis of the morphology and molecular analysis of the internal transcribed spacer (ITS), rpb2, and tef1-α genes. To test T. asperelloides TSU1-produced volatile organic compounds (VOCs) with antifungal activity, the sealed plate method was used. The VOCs of T. asperelloides TSU1 inhibited the mycelial growth of fungal pathogens that were recently reported as emerging diseases in Thailand, namely, Corynespora cassiicola, Fusarium incarnatum, Neopestalotiopsis clavispora, N. cubana, and Sclerotium rolfsii, with a percentage inhibition range of 38.88-68.33%. Solid-phase microextraction (SPME) was applied to trap VOCs from T. asperelloides TSU1 and tentatively identify them through gas chromatography-mass spectrometry (GC/MS). A total of 17 compounds were detected in the VOCs of T. asperelloides TSU1, and the dominant compounds were identified as fluoro(trinitro)methane (18.192% peak area) and 2-phenylethanol (9.803% peak area). Interestingly, the commercial 2-phenyethanol showed antifungal activity against fungal pathogens that were similar to the VOCs of T. asperelloides TSU1 by bioassay. On the basis of our study's results, T. asperelloides TSU1 isolated from soil displayed antifungal abilities via the production of VOCs responsible for restricting pathogen growth.
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13
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Yang Y, Sossah FL, Li Z, Hyde KD, Li D, Xiao S, Fu Y, Yuan X, Li Y. Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Mycogone perniciosa. Front Microbiol 2021; 11:596719. [PMID: 33505368 PMCID: PMC7829358 DOI: 10.3389/fmicb.2020.596719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/07/2020] [Indexed: 11/18/2022] Open
Abstract
Mycogone perniciosa causes wet bubble disease in Agaricus bisporus and various Agaricomycetes species. In a previous work, we identified 41 GH18 chitinase genes and other pathogenicity-related genes in the genome of M. perniciosa Hp10. Chitinases are enzymes that degrade chitin, and they have diverse functions in nutrition, morphogenesis, and pathogenesis. However, these important genes in M. perniciosa have not been fully characterized, and their functions remain unclear. Here, we performed a genome-wide analysis of M. perniciosa GH18 genes and analyzed the transcriptome profiles and GH18 expression patterns in M. perniciosa during the time course of infection in A. bisporus. Phylogenetic analysis of the 41 GH18 genes with those of 15 other species showed that the genes were clustered into three groups and eight subgroups based on their conserved domains. The GH18 genes clustered in the same group shared different gene structures but had the same protein motifs. All GH18 genes were localized in different organelles, were unevenly distributed on 11 contigs, and had orthologs in the other 13 species. Twelve duplication events were identified, and these had undergone both positive and purifying selection. The transcriptome analyses revealed that numerous genes, including transporters, cell wall degrading enzymes (CWDEs), cytochrome P450, pathogenicity-related genes, secondary metabolites, and transcription factors, were significantly upregulated at different stages of M. perniciosa Hp10 infection of A. bisporus. Twenty-three out of the 41 GH18 genes were differentially expressed. The expression patterns of the 23 GH18 genes were different and were significantly expressed from 3 days post-inoculation of M. perniciosa Hp10 in A. bisporus. Five differentially expressed GH18 genes were selected for RT-PCR and gene cloning to verify RNA-seq data accuracy. The results showed that those genes were successively expressed in different infection stages, consistent with the previous sequencing results. Our study provides a comprehensive analysis of pathogenicity-related and GH18 chitinase genes’ influence on M. perniciosa mycoparasitism of A. bisporus. Our findings may serve as a basis for further studies of M. perniciosa mycoparasitism, and the results have potential value for improving resistance in A. bisporus and developing efficient disease-management strategies to mitigate wet bubble disease.
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Affiliation(s)
- Yang Yang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,Guizhou Key Laboratory of Edible Fungi Breeding, Guizhou Academy of Agricultural Sciences, Guiyang, China.,College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Frederick Leo Sossah
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Zhuang Li
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai' an, China
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Dan Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,Guizhou Key Laboratory of Edible Fungi Breeding, Guizhou Academy of Agricultural Sciences, Guiyang, China.,College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Shijun Xiao
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Xiaohui Yuan
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,College of Plant Protection, Jilin Agricultural University, Changchun, China
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14
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Zúñiga-Silgado D, Rivera-Leyva JC, Coleman JJ, Sánchez-Reyez A, Valencia-Díaz S, Serrano M, de-Bashan LE, Folch-Mallol JL. Soil Type Affects Organic Acid Production and Phosphorus Solubilization Efficiency Mediated by Several Native Fungal Strains from Mexico. Microorganisms 2020; 8:E1337. [PMID: 32887277 DOI: 10.3390/microorganisms8091337] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/10/2023] Open
Abstract
Phosphorus (P) is considered a scarce macronutrient for plants in most tropical soils. The application of rock phosphate (RP) has been used to fertilize crops, but the amount of P released is not always at a necessary level for the plant. An alternative to this problem is the use of Phosphorus Solubilizing Microorganisms (PSM) to release P from chemically unavailable forms. This study compared the P sorption capacity of soils (the ability to retain P, making it unavailable for the plant) and the profile of organic acids (OA) produced by fungal isolates and the in vitro solubilization efficiency of RP. Trichoderma and Aspergillus strains were assessed in media with or without RP and different soils (Andisol, Alfisol, Vertisol). The type and amount of OA and the amount of soluble P were quantified, and according to our data, under the conditions tested, significant differences were observed in the OA profiles and the amount of soluble P present in the different soils. The efficiency to solubilize RP lies in the release of OAs with low acidity constants independent of the concentration at which they are released. It is proposed that the main mechanism of RP dissolution is the production of OAs.
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Mukherjee PK, Mehetre ST, Sherkhane PD, Muthukathan G, Ghosh A, Kotasthane AS, Khare N, Rathod P, Sharma KK, Nath R, Tewari AK, Bhattacharyya S, Arya M, Pathak D, Wasnikar AR, Tiwari RKS, Saxena DR. A Novel Seed-Dressing Formulation Based on an Improved Mutant Strain of Trichoderma virens, and Its Field Evaluation. Front Microbiol 2019; 10:1910. [PMID: 31543866 PMCID: PMC6730527 DOI: 10.3389/fmicb.2019.01910] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/05/2019] [Indexed: 11/13/2022] Open
Abstract
Using gamma-ray-induced mutagenesis, we have developed a mutant (named G2) of Trichoderma virens that produced two- to three-fold excesses of secondary metabolites, including viridin, viridiol, and some yet-to-be identified compounds. Consequently, this mutant had improved antibiosis against the oomycete test pathogen Pythium aphanidermatum. A transcriptome analysis of the mutant vis-à-vis the wild-type strain showed upregulation of several secondary-metabolism-related genes. In addition, many genes predicted to be involved in mycoparasitism and plant interactions were also upregulated. We used tamarind seeds as a mass multiplication medium in solid-state fermentation and, using talcum powder as a carrier, developed a novel seed dressing formulation. A comparative evaluation of the wild type and the mutant in greenhouse under high disease pressure (using the test pathogen Sclerotium rolfsii) revealed superiority of the mutant over wild type in protecting chickpea (Cicer arietinum) seeds and seedlings from infection. We then undertook extensive field evaluation (replicated micro-plot trials, on-farm demonstration trials, and large-scale trials in farmers' fields) of our mutant-based formulation (named TrichoBARC) for management of collar rot (S. rolfsii) in chickpea and lentil (Lens culinaris) over multiple locations in India. In certain experiments, other available formulations were included for comparison. This formulation consistently, over multiple locations and years, improved seed germination, reduced seedling mortality, and improved plant growth and yield. We also noticed growth promotion, improved pod bearing, and early flowering (7-10 days) in TrichoBARC-treated chickpea and lentil plants under field conditions. In toxicological studies in animal models, this formulation exhibited no toxicity to mammals, birds, or fish.
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Affiliation(s)
- Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sayaji T Mehetre
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - P D Sherkhane
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Gopi Muthukathan
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ananya Ghosh
- Department of Agronomy, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - A S Kotasthane
- Department of Plant Pathology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - N Khare
- Department of Plant Pathology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Parshuram Rathod
- Department of Plant Pathology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Kishan Kumar Sharma
- Department of Plant Pathology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Rajib Nath
- Department of Agronomy, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Anand K Tewari
- Department of Plant Pathology, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | | | - Meenakshi Arya
- Department of Plant Pathology, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - D Pathak
- Regional Agricultural Research Station, Assam Agricultural University, Shillongani, India
| | - A R Wasnikar
- Department of Plant Pathology, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur, India
| | - R K S Tiwari
- Department of Plant Pathology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - D R Saxena
- R.A.K. College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Sehore, India
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16
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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: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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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: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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. Electronic supplementary material The online version of this article (10.1186/s12864-019-5680-7) contains supplementary material, which is available to authorized users.
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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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18
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Ramírez-Valdespino CA, Casas-Flores S, Olmedo-Monfil V. Trichoderma as a Model to Study Effector-Like Molecules. Front Microbiol 2019; 10:1030. [PMID: 31156578 PMCID: PMC6529561 DOI: 10.3389/fmicb.2019.01030] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/24/2019] [Indexed: 11/24/2022] Open
Abstract
Plants are capable of perceiving microorganisms by coordinating processes to establish different forms of plant–microbe relationships. Plant colonization is governed in fungal and bacterial systems by secreted effector molecules, suppressing plant defense responses and modulating plant physiology to promote either virulence or compatibility. Proteins, secondary metabolites, and small RNAs have been described as effector molecules that use different mechanisms to establish the interaction. Effector molecules have been studied in more detail due to their involvement in harmful interactions, leading to a negative impact on agriculture. Recently, research groups have started to study the effectors in symbiotic interactions. Interestingly, most symbiotic effectors are members of the same families present in phytopathogens. Nevertheless, the quantity and ratio of secreted effectors depends on the microorganism and the host, suggesting a complex mechanism of recognition between the plant and their associated microorganisms. Fungi belonging to Trichoderma genus interact with plants by inducing their defense system and promoting plant growth. Research suggests that some of these effects are associated with effector molecules that Trichoderma delivers during the association with the plant. In this review, we will focus on the main findings concerning the effector molecules reported in Trichoderma spp. and their role during the interaction with plants, mainly in the molecular dialogue that takes place between them.
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Affiliation(s)
- Claudia A Ramírez-Valdespino
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Mexico.,Laboratorio de Biohidrometalurgia, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Mexico
| | - Sergio Casas-Flores
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, Mexico
| | - Vianey Olmedo-Monfil
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Mexico
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19
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Malinich EA, Wang K, Mukherjee PK, Kolomiets M, Kenerley CM. Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots. BMC Genomics 2019; 20:280. [PMID: 30971198 PMCID: PMC6458689 DOI: 10.1186/s12864-019-5651-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 03/27/2019] [Indexed: 12/16/2022] Open
Abstract
Background Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-industrial products. To better take advantage of this fungal-plant symbiosis it is necessary to obtain detailed knowledge of which genes Trichoderma utilizes during interaction with its plant host. In this study, we explored the transcriptional activity undergone by T. virens during two phases of symbiosis with maize; recognition of roots and after ingress into the root cortex. Results We present a model of T. virens – maize interaction wherein T. virens experiences global repression of transcription upon recognition of maize roots and then induces expression of a broad spectrum of genes during colonization of maize roots. The genes expressed indicate that, during colonization of maize roots, T. virens modulates biosynthesis of phytohormone-like compounds, secretes a plant-environment specific array of cell wall degrading enzymes and secondary metabolites, remodels both actin-based and cell membrane structures, and shifts metabolic activity. We also highlight transcription factors and signal transduction genes important in future research seeking to unravel the molecular mechanisms of T. virens activity in maize roots. Conclusions T. virens displays distinctly different transcriptional profiles between recognizing the presence of maize roots and active colonization of these roots. A though understanding of these processes will allow development of T. virens as a bio-control agent. Further, the publication of these datasets will target future research endeavors specifically to genes of interest when considering T. virens – maize symbiosis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5651-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth A Malinich
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Ken Wang
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Prasun K Mukherjee
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Michael Kolomiets
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Charles M Kenerley
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
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20
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Abstract
Plants are capable of perceiving microorganisms by coordinating processes to establish different forms of plant-microbe relationships. Plant colonization is governed in fungal and bacterial systems by secreted effector molecules, suppressing plant defense responses and modulating plant physiology to promote either virulence or compatibility. Proteins, secondary metabolites, and small RNAs have been described as effector molecules that use different mechanisms to establish the interaction. Effector molecules have been studied in more detail due to their involvement in harmful interactions, leading to a negative impact on agriculture. Recently, research groups have started to study the effectors in symbiotic interactions. Interestingly, most symbiotic effectors are members of the same families present in phytopathogens. Nevertheless, the quantity and ratio of secreted effectors depends on the microorganism and the host, suggesting a complex mechanism of recognition between the plant and their associated microorganisms. Fungi belonging to Trichoderma genus interact with plants by inducing their defense system and promoting plant growth. Research suggests that some of these effects are associated with effector molecules that Trichoderma delivers during the association with the plant. In this review, we will focus on the main findings concerning the effector molecules reported in Trichoderma spp. and their role during the interaction with plants, mainly in the molecular dialogue that takes place between them.
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Affiliation(s)
- Claudia A Ramírez-Valdespino
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Mexico
- Laboratorio de Biohidrometalurgia, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Mexico
| | - Sergio Casas-Flores
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, Mexico
| | - Vianey Olmedo-Monfil
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Mexico
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21
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Manganiello G, Sacco A, Ercolano MR, Vinale F, Lanzuise S, Pascale A, Napolitano M, Lombardi N, Lorito M, Woo SL. Modulation of Tomato Response to Rhizoctonia solani by Trichoderma harzianum and Its Secondary Metabolite Harzianic Acid. Front Microbiol 2018; 9:1966. [PMID: 30233507 PMCID: PMC6127634 DOI: 10.3389/fmicb.2018.01966] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/02/2018] [Indexed: 01/25/2023] Open
Abstract
The present study investigated the transcriptomic and metabolomic changes elicited in tomato plants (Solanum lycopersicum cv. Micro-Tom) following treatments with the biocontrol agent Trichoderma harzianum strain M10 or its purified secondary metabolite harzianic acid (HA), in the presence or the absence of the soil-borne pathogen Rhizoctonia solani. Transcriptomic analysis allowed the identification of differentially expressed genes (DEGs) that play a pivotal role in resistance to biotic stress. Overall, the results support the ability of T. harzianum M10 to activate defense responses in infected tomato plants. An induction of hormone-mediated signaling was observed, as shown by the up-regulation of genes involved in the ethylene and jasmonate (ET/JA) and salicylic acid (SA)-mediated signaling pathways. Further, the protective action of T. harzianum on the host was revealed by the over-expression of genes able to detoxify cells from reactive oxygen species (ROS). On the other hand, HA treatment also stimulated tomato response to the pathogen by inducing the expression of several genes involved in defense response (including protease inhibitors, resistance proteins like CC-NBS-LRR) and hormone interplay. The accumulation of steroidal glycoalkaloids in the plant after treatments with either T. harzianum or HA, as determined by metabolomic analysis, confirmed the complexity of the plant response to beneficial microbes, demonstrating that these microorganisms are also capable of activating the chemical defenses.
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Affiliation(s)
- Gelsomina Manganiello
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Adriana Sacco
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Maria R. Ercolano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Francesco Vinale
- National Research Council, Institute for Sustainable Plant Protection, Portici, Italy
| | - Stefania Lanzuise
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Alberto Pascale
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Mauro Napolitano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Nadia Lombardi
- National Research Council, Institute for Sustainable Plant Protection, Portici, Italy
| | - Matteo Lorito
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- National Research Council, Institute for Sustainable Plant Protection, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Sheridan L. Woo
- National Research Council, Institute for Sustainable Plant Protection, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ramírez-Valdespino CA, Porras-Troncoso MD, Corrales-Escobosa AR, Wrobel K, Martínez-Hernández P, Olmedo-Monfil V. Functional Characterization of TvCyt2, a Member of the p450 Monooxygenases From Trichoderma virens Relevant During the Association With Plants and Mycoparasitism. Mol Plant Microbe Interact 2018; 31:289-298. [PMID: 29256741 DOI: 10.1094/mpmi-01-17-0015-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Secondary metabolites are crucial for the establishment of interactions between plants and microbes, as in the case of Trichoderma-plant interactions. In the biosynthetic pathway of secondary metabolites, specific enzymes participate in the formation of hydroxyl and epoxy groups, belonging to the p450 monooxygenases family. Here, we show that the product of the gene TvCyt2 from Trichoderma virens encodes a new protein homologous to the cytochrome p450, which is down-regulated at the beginning of Trichoderma-Arabidopsis interaction. To investigate its role in the interactions established by Trichoderma spp., we analyzed the metabolic profile obtained from the overexpressing (OETvCyt2) and null mutant (Δtvcyt2) strains, observing that the OETvCyt2 strains produce a higher concentration of some metabolites than the wild-type (WT) strain. Δtvcyt2 strains showed a decreased antagonistic activity against Rhizoctonia solani in antibiosis assays. Arabidopsis plants cocultivated with the OETvCyt2 strains showed stronger induction of systemic acquired resistance than plants cocultivated with the WT strain, as well as increases in biomass and fitness. Our data suggest that the product of the TvCyt2 gene is involved in secondary metabolite biosynthesis, which can increase antagonistic activity with phytopathogenic fungi and the capacity to promote plant growth.
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Affiliation(s)
- Claudia A Ramírez-Valdespino
- 1 Universidad de Guanajuato, División de Ciencias Naturales y Exactas, Departamento de Biología, Guanajuato, Gto. México
| | - Maria Daniela Porras-Troncoso
- 1 Universidad de Guanajuato, División de Ciencias Naturales y Exactas, Departamento de Biología, Guanajuato, Gto. México
| | - Alma Rosa Corrales-Escobosa
- 2 Universidad de Guanajuato, División de Ciencias Naturales y Exactas, Departamento de Química, Guanajuato, Gto. México; and
| | - Kazimierz Wrobel
- 2 Universidad de Guanajuato, División de Ciencias Naturales y Exactas, Departamento de Química, Guanajuato, Gto. México; and
| | - Pedro Martínez-Hernández
- 3 Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y Estudios Avanzados del IPN, Irapuato, Gto. México
| | - Vianey Olmedo-Monfil
- 1 Universidad de Guanajuato, División de Ciencias Naturales y Exactas, Departamento de Biología, Guanajuato, Gto. México
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Mendoza-mendoza A, Zaid R, Lawry R, Hermosa R, Monte E, Horwitz BA, Mukherjee PK. Molecular dialogues between Trichoderma and roots: Role of the fungal secretome. FUNGAL BIOL REV 2018; 32:62-85. [DOI: 10.1016/j.fbr.2017.12.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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25
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Nogueira-Lopez G, Greenwood DR, Middleditch M, Winefield C, Eaton C, Steyaert JM, Mendoza-Mendoza A. The Apoplastic Secretome of Trichoderma virens During Interaction With Maize Roots Shows an Inhibition of Plant Defence and Scavenging Oxidative Stress Secreted Proteins. Front Plant Sci 2018; 9:409. [PMID: 29675028 PMCID: PMC5896443 DOI: 10.3389/fpls.2018.00409] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/14/2018] [Indexed: 05/04/2023]
Abstract
In Nature, almost every plant is colonized by fungi. Trichoderma virens is a biocontrol fungus which has the capacity to behave as an opportunistic plant endophyte. Even though many plants are colonized by this symbiont, the exact mechanisms by which Trichoderma masks its entrance into its plant host remain unknown, but likely involve the secretion of different families of proteins into the apoplast that may play crucial roles in the suppression of plant immune responses. In this study, we investigated T. virens colonization of maize roots under hydroponic conditions, evidencing inter- and intracellular colonization by the fungus and modifications in root morphology and coloration. Moreover, we show that upon host penetration, T. virens secretes into the apoplast an arsenal of proteins to facilitate inter- and intracellular colonization of maize root tissues. Using a gel-free shotgun proteomics approach, 95 and 43 secretory proteins were identified from maize and T. virens, respectively. A reduction in the maize secretome (36%) was induced by T. virens, including two major groups, glycosyl hydrolases and peroxidases. Furthermore, T. virens secreted proteins were mainly involved in cell wall hydrolysis, scavenging of reactive oxygen species and secondary metabolism, as well as putative effector-like proteins. Levels of peroxidase activity were reduced in the inoculated roots, suggesting a strategy used by T. virens to manipulate host immune responses. The results provide an insight into the crosstalk in the apoplast which is essential to maintain the T. virens-plant interaction.
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Affiliation(s)
| | - David R. Greenwood
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Martin Middleditch
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Christopher Winefield
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Carla Eaton
- Bio-Protection Research Centre, New Zealand and Institute of Fundamental Sciences, Massey University, Wellington, New Zealand
| | | | - Artemio Mendoza-Mendoza
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
- *Correspondence: Artemio Mendoza-Mendoza
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26
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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: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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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. Mol Plant Pathol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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29
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Contreras-Cornejo HA, Macías-Rodríguez L, del-Val E, Larsen J. Ecological functions ofTrichodermaspp. and their secondary metabolites in the rhizosphere: interactions with plants. FEMS Microbiol Ecol 2016; 92:fiw036. [DOI: 10.1093/femsec/fiw036] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2016] [Indexed: 01/23/2023] Open
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