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French KS, Chukwuma E, Linshitz I, Namba K, Duckworth OW, Cubeta MA, Baars O. Inactivation of siderophore iron-chelating moieties by the fungal wheat root symbiont Pyrenophora biseptata. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13234. [PMID: 38240404 PMCID: PMC10866069 DOI: 10.1111/1758-2229.13234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/28/2023] [Indexed: 02/15/2024]
Abstract
We investigated the ability of four plant and soil-associated fungi to modify or degrade siderophore structures leading to reduced siderophore iron-affinity in iron-limited and iron-replete cultures. Pyrenophora biseptata, a melanized fungus from wheat roots, was effective in inactivating siderophore iron-chelating moieties. In the supernatant solution, the tris-hydroxamate siderophore desferrioxamine B (DFOB) underwent a stepwise reduction of the three hydroxamate groups in DFOB to amides leading to a progressive loss in iron affinity. A mechanism is suggested based on the formation of transient ferrous iron followed by reduction of the siderophore hydroxamate groups during fungal high-affinity reductive iron uptake. P. biseptata also produced its own tris-hydroxamate siderophores (neocoprogen I and II, coprogen and dimerum acid) in iron-limited media and we observed loss of hydroxamate chelating groups during incubation in a manner analogous to DFOB. A redox-based reaction was also involved with the tris-catecholate siderophore protochelin in which oxidation of the catechol groups to quinones was observed. The new siderophore inactivating activity of the wheat symbiont P. biseptata is potentially widespread among fungi with implications for the availability of iron to plants and the surrounding microbiome in siderophore-rich environments.
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Affiliation(s)
- Katie S. French
- Department of Entomology and Plant PathologyNorth Carolina State University, Center for Integrated Fungal ResearchRaleighNorth CarolinaUSA
- Present address:
Department of Soil ScienceUniversity of ArkansasFayettevilleArkansasUSA
| | - Emmanuel Chukwuma
- Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Ilan Linshitz
- Department of BiologyUniversity of MarylandCollege ParkMarylandUSA
| | - Kosuke Namba
- Department of Pharmaceutical SciencesTokushima UniversityTokushimaJapan
| | - Owen W. Duckworth
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Marc A. Cubeta
- Department of Entomology and Plant PathologyNorth Carolina State University, Center for Integrated Fungal ResearchRaleighNorth CarolinaUSA
| | - Oliver Baars
- Department of Entomology and Plant PathologyNorth Carolina State University, Center for Integrated Fungal ResearchRaleighNorth CarolinaUSA
- Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
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2
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Ferreira NCDF, Ramos MLG, Gatto A. Use of Trichoderma in the Production of Forest Seedlings. Microorganisms 2024; 12:237. [PMID: 38399641 PMCID: PMC10893047 DOI: 10.3390/microorganisms12020237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 02/25/2024] Open
Abstract
Forest production has great relevance in the Brazilian economy, characterized by several production sectors, including the production of seedlings. With the focus on maximizing the capacity of survival, development, and adaptation of seedlings, Trichoderma is highlighted as a potentially useful genus of microorganisms for promoting growth and higher product quality. In this sense, this review aims to describe the main mechanisms of fungi action in forest seedlings' production. The different species of the genus Trichoderma have specific mechanisms of action, and the current scenario points to more advances in the number of species. The interaction process mediated by different mechanisms of action begins in the communication with plants, from the colonization process. After the interaction, chemical dialogues allow the plant to develop better because, from colonization, the forest seedlings can maximize height and increase shoot and root development. Fungi promote solubilization and availability of nutrients to seedlings, which show numerous benefits to the development. The use of beneficial microorganisms, such as fungi of the genus Trichoderma, has become a sustainable strategy to enhance seedling development, reducing the use of agrochemicals and industrial fertilizers.
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Affiliation(s)
| | | | - Alcides Gatto
- Department of Forestry Engineering, Faculty of Technology, University of Brasilia, Brasilia 70910-900, DF, Brazil
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3
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Villalobos-Escobedo JM, Mercado-Esquivias MB, Adams C, Kauffman WB, Malmstrom RR, Deutschbauer AM, Glass NL. Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites. PLoS Genet 2023; 19:e1010909. [PMID: 37651474 PMCID: PMC10516422 DOI: 10.1371/journal.pgen.1010909] [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: 04/23/2023] [Revised: 09/22/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023] Open
Abstract
Trichoderma spp. are ubiquitous rhizosphere fungi capable of producing several classes of secondary metabolites that can modify the dynamics of the plant-associated microbiome. However, the bacterial-fungal mechanisms that mediate these interactions have not been fully characterized. Here, a random barcode transposon-site sequencing (RB-TnSeq) approach was employed to identify bacterial genes important for fitness in the presence of Trichoderma atroviride exudates. We selected three rhizosphere bacteria with RB-TnSeq mutant libraries that can promote plant growth: the nitrogen fixers Klebsiella michiganensis M5aI and Herbaspirillum seropedicae SmR1, and Pseudomonas simiae WCS417. As a non-rhizosphere species, Pseudomonas putida KT2440 was also included. From the RB-TnSeq data, nitrogen-fixing bacteria competed mainly for iron and required the siderophore transport system TonB/ExbB for optimal fitness in the presence of T. atroviride exudates. In contrast, P. simiae and P. putida were highly dependent on mechanisms associated with membrane lipid modification that are required for resistance to cationic antimicrobial peptides (CAMPs). A mutant in the Hog1-MAP kinase (Δtmk3) gene of T. atroviride showed altered expression patterns of many nonribosomal peptide synthetase (NRPS) biosynthetic gene clusters with potential antibiotic activity. In contrast to exudates from wild-type T. atroviride, bacterial mutants containing lesions in genes associated with resistance to antibiotics did not show fitness defects when RB-TnSeq libraries were exposed to exudates from the Δtmk3 mutant. Unexpectedly, exudates from wild-type T. atroviride and the Δtmk3 mutant rescued purine auxotrophic mutants of H. seropedicae, K. michiganensis and P. simiae. Metabolomic analysis on exudates from wild-type T. atroviride and the Δtmk3 mutant showed that both strains excrete purines and complex metabolites; functional Tmk3 is required to produce some of these metabolites. This study highlights the complex interplay between Trichoderma-metabolites and soil bacteria, revealing both beneficial and antagonistic effects, and underscoring the intricate and multifaceted nature of this relationship.
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Affiliation(s)
- José Manuel Villalobos-Escobedo
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Maria Belen Mercado-Esquivias
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Catharine Adams
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - W. Berkeley Kauffman
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Rex R. Malmstrom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam M. Deutschbauer
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - N. Louise Glass
- Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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4
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Timofeeva AM, Galyamova MR, Sedykh SE. Bacterial Siderophores: Classification, Biosynthesis, Perspectives of Use in Agriculture. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223065. [PMID: 36432794 PMCID: PMC9694258 DOI: 10.3390/plants11223065] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 06/07/2023]
Abstract
Siderophores are synthesized and secreted by many bacteria, yeasts, fungi, and plants for Fe (III) chelation. A variety of plant-growth-promoting bacteria (PGPB) colonize the rhizosphere and contribute to iron assimilation by plants. These microorganisms possess mechanisms to produce Fe ions under iron-deficient conditions. Under appropriate conditions, they synthesize and release siderophores, thereby increasing and regulating iron bioavailability. This review focuses on various bacterial strains that positively affect plant growth and development through synthesizing siderophores. Here we discuss the diverse chemical nature of siderophores produced by plant root bacteria; the life cycle of siderophores, from their biosynthesis to the Fe-siderophore complex degradation; three mechanisms of siderophore biosynthesis in bacteria; the methods for analyzing siderophores and the siderophore-producing activity of bacteria and the methods for screening the siderophore-producing activity of bacterial colonies. Further analysis of biochemical, molecular-biological, and physiological features of siderophore synthesis by bacteria and their use by plants will allow one to create effective microbiological preparations for improving soil fertility and increasing plant biomass, which is highly relevant for sustainable agriculture.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia
| | - Maria R. Galyamova
- Center for Entrepreneurial Initiatives, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Martinet L, Baiwir D, Mazzucchelli G, Rigali S. Structure of New Ferroverdins Recruiting Unconventional Ferrous Iron Chelating Agents. Biomolecules 2022; 12:biom12060752. [PMID: 35740878 PMCID: PMC9221444 DOI: 10.3390/biom12060752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Ferroverdins are ferrous iron (Fe2+)-nitrosophenolato complexes produced by a few Streptomyces species as a response to iron overload. Previously, three ferroverdins were identified: ferroverdin A, in which three molecules of p-vinylphenyl-3-nitroso-4-hydroxybenzoate (p-vinylphenyl-3,4-NHBA) are recruited to bind Fe2+, and Ferroverdin B and Ferroverdin C, in which one molecule of p-vinylphenyl-3,4-NHBA is substituted by hydroxy-p-vinylphenyl-3,4-NHBA, and by carboxy-p-vinylphenyl-3,4-NHBA, respectively. These molecules, especially ferroverdin B, are potent inhibitors of the human cholesteryl ester transfer protein (CETP) and therefore candidate hits for the development of drugs that increase the serum concentration of high-density lipoprotein cholesterol, thereby diminishing the risk of atherosclerotic cardiovascular disease. In this work, we used high-resolution mass spectrometry combined with tandem mass spectrometry to identify 43 novel ferroverdins from the cytosol of two Streptomyces lunaelactis species. For 13 of them (designated ferroverdins C2, C3, D, D2, D3, E, F, G, H, CD, DE, DF, and DG), we could elucidate their structure, and for the other 17 new ferroverdins, ambiguity remains for one of the three ligands. p-formylphenyl-3,4-NHBA, p-benzoic acid-3,4-NHBA, 3,4-NHBA, p-phenylpropionate-3,4-NHBA, and p-phenyacetate-3,4-NHBA were identified as new alternative chelators for Fe2+-binding, and two compounds (C3 and D3) are the first reported ferroverdins that do not recruit p-vinylphenyl-3,4-NHBA. Our work thus uncovered putative novel CETP inhibitors or ferroverdins with novel bioactivities.
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Affiliation(s)
- Loïc Martinet
- InBioS, Center for Protein Engineering, University of Liege, B-4000 Liege, Belgium
- Hedera-22, Boulevard du Rectorat 27b, B-4000 Liege, Belgium;
| | - Dominique Baiwir
- GIGA Proteomics Facility, University of Liege, B-4000 Liege, Belgium;
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, B-4000 Liege, Belgium;
| | - Sébastien Rigali
- InBioS, Center for Protein Engineering, University of Liege, B-4000 Liege, Belgium
- Hedera-22, Boulevard du Rectorat 27b, B-4000 Liege, Belgium;
- Correspondence:
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6
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Contreras-Cornejo HA, Macías-Rodríguez L, Larsen J. The Role of Secondary Metabolites in Rhizosphere Competence of Trichoderma. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_6] [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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7
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Industrially Important Genes from Trichoderma. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_16] [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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8
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González Y, de los Santos-Villalobos S, Castro-Longoria E. Trichoderma Secondary Metabolites Involved in Microbial Inhibition. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Sarrocco S, Vicente I, Staropoli A, Vinale F. Genes Involved in the Secondary Metabolism of Trichoderma and the Biochemistry of These Compounds. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Kang S, Lumactud R, Li N, Bell TH, Kim HS, Park SY, Lee YH. Harnessing Chemical Ecology for Environment-Friendly Crop Protection. PHYTOPATHOLOGY 2021; 111:1697-1710. [PMID: 33908803 DOI: 10.1094/phyto-01-21-0035-rvw] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant-microbe and microbe-microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.
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Affiliation(s)
- Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Rhea Lumactud
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Ningxiao Li
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Hye-Seon Kim
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL 61604, U.S.A
| | - Sook-Young Park
- Department of Agricultural Life Science, Sunchon National University, Suncheon 57922, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
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11
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Boysen JM, Saeed N, Hillmann F. Natural products in the predatory defence of the filamentous fungal pathogen Aspergillus fumigatus. Beilstein J Org Chem 2021; 17:1814-1827. [PMID: 34394757 PMCID: PMC8336654 DOI: 10.3762/bjoc.17.124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/14/2021] [Indexed: 11/30/2022] Open
Abstract
The kingdom of fungi comprises a large and highly diverse group of organisms that thrive in diverse natural environments. One factor to successfully confront challenges in their natural habitats is the capability to synthesize defensive secondary metabolites. The genetic potential for the production of secondary metabolites in fungi is high and numerous potential secondary metabolite gene clusters have been identified in sequenced fungal genomes. Their production may well be regulated by specific ecological conditions, such as the presence of microbial competitors, symbionts or predators. Here we exemplarily summarize our current knowledge on identified secondary metabolites of the pathogenic fungus Aspergillus fumigatus and their defensive function against (microbial) predators.
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Affiliation(s)
- Jana M Boysen
- Junior Research Group Evolution of Microbial Interactions, Leibniz-Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Nauman Saeed
- Junior Research Group Evolution of Microbial Interactions, Leibniz-Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interactions, Leibniz-Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
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12
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Madbouly AK. Biodiversity of Genus Trichoderma and Their Potential Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-67561-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Kügler S, Cooper RE, Boessneck J, Küsel K, Wichard T. Rhizobactin B is the preferred siderophore by a novel Pseudomonas isolate to obtain iron from dissolved organic matter in peatlands. Biometals 2020; 33:415-433. [PMID: 33026607 PMCID: PMC7676072 DOI: 10.1007/s10534-020-00258-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/30/2020] [Indexed: 01/12/2023]
Abstract
Bacteria often release diverse iron-chelating compounds called siderophores to scavenge iron from the environment for many essential biological processes. In peatlands, where the biogeochemical cycle of iron and dissolved organic matter (DOM) are coupled, bacterial iron acquisition can be challenging even at high total iron concentrations. We found that the bacterium Pseudomonas sp. FEN, isolated from an Fe-rich peatland in the Northern Bavarian Fichtelgebirge (Germany), released an unprecedented siderophore for its genus. High-resolution mass spectrometry (HR-MS) using metal isotope-coded profiling (MICP), MS/MS experiments, and nuclear magnetic resonance spectroscopy (NMR) identified the amino polycarboxylic acid rhizobactin and a novel derivative at even higher amounts, which was named rhizobactin B. Interestingly, pyoverdine-like siderophores, typical for this genus, were not detected. With peat water extract (PWE), studies revealed that rhizobactin B could acquire Fe complexed by DOM, potentially through a TonB-dependent transporter, implying a higher Fe binding constant of rhizobactin B than DOM. The further uptake of Fe-rhizobactin B by Pseudomonas sp. FEN suggested its role as a siderophore. Rhizobactin B can complex several other metals, including Al, Cu, Mo, and Zn. The study demonstrates that the utilization of rhizobactin B can increase the Fe availability for Pseudomonas sp. FEN through ligand exchange with Fe-DOM, which has implications for the biogeochemical cycling of Fe in this peatland.
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Affiliation(s)
- Stefan Kügler
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Rebecca E Cooper
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Johanna Boessneck
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
- The German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany.
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Vinale F, Sivasithamparam K. Beneficial effects of Trichoderma secondary metabolites on crops. Phytother Res 2020; 34:2835-2842. [PMID: 32578292 DOI: 10.1002/ptr.6728] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022]
Abstract
Selected microbial strains used as active ingredients of biopesticides for agricultural management practices (e.g., IPM, Integrated Pest Management) are known for their ability to control phytopathogens, promote plant growth, and/or induce disease resistance. Microbes belonging to the Trichoderma genus are considered as an appropriate example of beneficial microbes and are model organisms to study plant-microbe interactions. Several Trichoderma strains are marketed as biocontrol agents and are known to increase plant growth, stress tolerance, and nutrient availability. These effects have sometimes been related to the production of effector metabolites that beneficial microbes produce during the interaction with plant and other microbes. Secondary metabolites (SMs) comprise different classes of natural compounds with low molecular weight and having numerous biological roles, especially in the interactions among organisms. Metabolomic analysis of the interactions between plants, phytopathogens, and beneficial fungi aided in the identification of several bioactive fungal SMs that positively affect plant metabolism. Some of these compounds showed direct activity against phytopathogens, but also increased disease resistance by triggering the plant defence system, and/or enhanced vegetative growth. A new generation of bioformulations based on microbial metabolites and living consortia responsible for the desired beneficial effects on crops may overcome the difficulties associated with the use of a single living microbial strain.
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Affiliation(s)
- Francesco Vinale
- Department of Veterinary Medicine and Animal Production, University of Naples 'Federico II', Naples, Italy.,CNR Institute for Sustainable Plant Protection, Portici, Italy
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15
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Coninck E, Scauflaire J, Gollier M, Liénard C, Foucart G, Manssens G, Munaut F, Legrève A. Trichoderma atroviride as a promising biocontrol agent in seed coating for reducing Fusarium damping-off on maize. J Appl Microbiol 2020; 129:637-651. [PMID: 32181551 DOI: 10.1111/jam.14641] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/13/2020] [Accepted: 03/10/2020] [Indexed: 11/26/2022]
Abstract
AIMS The objective of this work was to identify a fungal strain showing potential biocontrol abilities against two Fusarium damping-off agents and to test it as a Biological Control Agent (BCA) in maize seed coating under field conditions. METHODS AND RESULTS A collection of native fungal strains associated with maize in Belgium was screened for antagonistic potential against Fusarium avenaceum and Fusarium culmorum. The strain with highest biocontrol potential was identified as an endophytic Trichoderma atroviride BC0584. In greenhouse, it significantly improves the emergence of seedlings infected by F. avenaceum or F. culmorum pathogens. In most field trials carried out during the season 2017, it significantly increased the emergence rate of infected seedlings compared to untreated seeds. One slurriable powder formulation allows BCA conidia to survive over a 6-month storage period at 4°C. CONCLUSIONS The fungal BC0584 strain is a promising BCA that could be an alternative to synthetic fungicides. It is adapted to local environmental conditions, is easily and cheaply produced and can be stored in a low-cost formulation. SIGNIFICANCE AND IMPACT OF THE STUDY In Belgium, this is the first study to use a T. atroviride native strain against Fusarium damping-off on maize crop. Modes of action and required conditions for ensuring high biocontrol activity in the field have still to be investigated.
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Affiliation(s)
- E Coninck
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - J Scauflaire
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - M Gollier
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - C Liénard
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - G Foucart
- Centre Indépendant de Promotion Fourragère (CIPF), Louvain-la-Neuve, Belgium
| | - G Manssens
- Centre Indépendant de Promotion Fourragère (CIPF), Louvain-la-Neuve, Belgium
| | - F Munaut
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - A Legrève
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
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16
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Towards the Biological Control of Devastating Forest Pathogens from the Genus Armillaria. FORESTS 2019. [DOI: 10.3390/f10111013] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Research Highlights: A large scale effort to screen, characterize, and select Trichoderma strains with the potential to antagonize Armillaria species revealed promising candidates for field applications. Background and Objectives: Armillaria species are among the economically most relevant soilborne tree pathogens causing devastating root diseases worldwide. Biocontrol agents are environment-friendly alternatives to chemicals in restraining the spread of Armillaria in forest soils. Trichoderma species may efficiently employ diverse antagonistic mechanisms against fungal plant pathogens. The aim of this paper is to isolate indigenous Trichoderma strains from healthy and Armillaria-damaged forests, characterize them, screen their biocontrol properties, and test selected strains under field conditions. Materials and Methods: Armillaria and Trichoderma isolates were collected from soil samples of a damaged Hungarian oak and healthy Austrian spruce forests and identified to the species level. In vitro antagonism experiments were performed to determine the potential of the Trichoderma isolates to control Armillaria species. Selected biocontrol candidates were screened for extracellular enzyme production and plant growth-promoting traits. A field experiment was carried out by applying two selected Trichoderma strains on two-year-old European Turkey oak seedlings planted in a forest area heavily overtaken by the rhizomorphs of numerous Armillaria colonies. Results: Although A. cepistipes and A. ostoyae were found in the Austrian spruce forests, A. mellea and A. gallica clones dominated the Hungarian oak stand. A total of 64 Trichoderma isolates belonging to 14 species were recovered. Several Trichoderma strains exhibited in vitro antagonistic abilities towards Armillaria species and produced siderophores and indole-3-acetic acid. Oak seedlings treated with T. virens and T. atrobrunneum displayed better survival under harsh soil conditions than the untreated controls. Conclusions: Selected native Trichoderma strains, associated with Armillaria rhizomorphs, which may also have plant growth promoting properties, are potential antagonists of Armillaria spp., and such abilities can be exploited in the biological control of Armillaria root rot.
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Antimicrobial secondary metabolites from agriculturally important fungi as next biocontrol agents. Appl Microbiol Biotechnol 2019; 103:9287-9303. [DOI: 10.1007/s00253-019-10209-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/15/2019] [Accepted: 10/19/2019] [Indexed: 10/25/2022]
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18
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Gledhill M, Basu S, Shaked Y. Metallophores associated with Trichodesmium erythraeum colonies from the Gulf of Aqaba. Metallomics 2019; 11:1547-1557. [PMID: 31475278 DOI: 10.1039/c9mt00121b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trichodesmium is a globally important marine nitrogen fixing cyanobacteria which forms colonies and utilizes atmospherically derived dust as a source for the limiting micro-nutrient iron. Here we report the identification of metallophores isolated from incubations of natural Trichodesmium colonies collected from the Gulf of Aqaba in the Red Sea. Three of our compounds were identified as the ferrioxamine siderophores B, E, and G. The remaining fifteen metallophores had mass to charge ratios that, to our knowledge, are not common to known siderophores. Putative sum formulas suggest most of these compounds were not structurally related to each other. We also found that the novel metallophores readily formed complexes with aluminium and were less specific for iron than the ferrioxamines. In our incubations of Trichodesmium colonies, the abundance of ten of the novel metallophores positively correlated with Trichodesmium biomass, but not with bacterial biomass, whilst ferrioxamine siderophores were more strongly associated with bacterial biomass. We identified ferrioxamines and our novel metallophores in filtered surface seawater samples from the Gulf of Aqaba. However, our novel metallophores were only observed in the surface seawater sample collected at the time of highest Trichodesmium abundance, while ferrioxamines were observed even when Trichodesmium was not present. We hypothesize that the novel metallophores were specifically associated with Trichodesmium colonies. Together with the bacterially produced ferrioxamines they likely contribute to a distinctive "ligandosphere" surrounding the Trichodesmium colonies, with potential implications for metal homeostasis within the colony environment.
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Affiliation(s)
- Martha Gledhill
- GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, Germany.
| | - Subhajit Basu
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel and The Interuniversity Institute for Marine Sciences in Eilat, Eilat 88103, Israel
| | - Yeala Shaked
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel and The Interuniversity Institute for Marine Sciences in Eilat, Eilat 88103, Israel
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Hitzenhammer E, Büschl C, Sulyok M, Schuhmacher R, Kluger B, Wischnitzki E, Schmoll M. YPR2 is a regulator of light modulated carbon and secondary metabolism in Trichoderma reesei. BMC Genomics 2019; 20:211. [PMID: 30866811 PMCID: PMC6417087 DOI: 10.1186/s12864-019-5574-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/28/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Filamentous fungi have evolved to succeed in nature by efficient growth and degradation of substrates, but also due to the production of secondary metabolites including mycotoxins. For Trichoderma reesei, as a biotechnological workhorse for homologous and heterologous protein production, secondary metabolite secretion is of particular importance for industrial application. Recent studies revealed an interconnected regulation of enzyme gene expression and carbon metabolism with secondary metabolism. RESULTS Here, we investigated gene regulation by YPR2, one out of two transcription factors located within the SOR cluster of T. reesei, which is involved in biosynthesis of sorbicillinoids. Transcriptome analysis showed that YPR2 exerts its major function in constant darkness upon growth on cellulose. Targets (direct and indirect) of YPR2 overlap with induction specific genes as well as with targets of the carbon catabolite repressor CRE1 and a considerable proportion is regulated by photoreceptors as well. Functional category analysis revealed both effects on carbon metabolism and secondary metabolism. Further, we found indications for an involvement of YPR2 in regulation of siderophores. In agreement with transcriptome data, mass spectrometric analyses revealed a broad alteration in metabolite patterns in ∆ypr2. Additionally, YPR2 positively influenced alamethicin levels along with transcript levels of the alamethicin synthase tex1 and is essential for production of orsellinic acid in darkness. CONCLUSIONS YPR2 is an important regulator balancing secondary metabolism with carbon metabolism in darkness and depending on the carbon source. The function of YPR2 reaches beyond the SOR cluster in which ypr2 is located and happens downstream of carbon catabolite repression mediated by CRE1.
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Affiliation(s)
- Eva Hitzenhammer
- AIT - Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Christoph Büschl
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Michael Sulyok
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Bernhard Kluger
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Elisabeth Wischnitzki
- AIT - Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Monika Schmoll
- AIT - Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
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20
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Palyzová A, Svobodová K, Sokolová L, Novák J, Novotný Č. Metabolic profiling of Fusarium oxysporum f. sp. conglutinans race 2 in dual cultures with biocontrol agents Bacillus amyloliquefaciens, Pseudomonas aeruginosa, and Trichoderma harzianum. Folia Microbiol (Praha) 2019; 64:779-787. [PMID: 30746611 DOI: 10.1007/s12223-019-00690-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/05/2019] [Indexed: 11/26/2022]
Abstract
There are increasing efforts to identify biocontrol-active microbial metabolites in order to improve strategies for biocontrol of phytopathogens. In this work, Fusarium oxysporum f. sp. conglutinans was confronted with three different biocontrol agents: Trichoderma harzianum, Bacillus amyloliquefaciens, and Pseudomonas aeruginosa in dual culture bioassays. Metabolites produced during the microbial interactions were screened by a matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). T. harzianum exhibited the strongest inhibition of growth of F. oxysporum resulting in overlay of the pathogen colony with its mycelium. Recorded metabolite profiles suggested a direct attack of F. oxysporum mycelium by T. harzianum and B. amyloliquefaciens by means of membrane-attacking peptaibols and a set of antimicrobial lipopeptides and siderophores, respectively. The direct mode of the biocontrol activity of T. harzianum and B. amyloliquefaciens corresponded to their ability to suppress F. oxysporum production of mycotoxin beauvericin suggesting that this ability is not specific only for Trichoderma species. In the case of P. aeruginosa, siderophores pyoverdine E/D and two rhamnolipids were produced as major bacterial metabolites; the rhamnolipid production was blocked by F. oxysporum. The results showed that this type of biocontrol activity was the least effective against F. oxysporum. The effective application of MALDI-MS profiling to the screening of nonvolatile microbial metabolites produced during the interaction of the phytopathogen and the biocontrol microorganisms was demonstrated.
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Affiliation(s)
- Andrea Palyzová
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Kateřina Svobodová
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Lucie Sokolová
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Jiří Novák
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Čeněk Novotný
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic.
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21
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Shinozaki Y, Kitamoto H, Sameshima-Yamashita Y, Kinoshita A, Nakajima-Kambe T. Isolation of a novel Co 2+-resistant bacterium and the application of its siderophore in Co 2+ recovery from an aqueous solution. J GEN APPL MICROBIOL 2019; 65:273-276. [DOI: 10.2323/jgam.2018.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yukiko Shinozaki
- Research Fellow of the Japan Society for the Promotion of Science
- National Institute for Agro-Environmental Sciences (NIAES)
| | | | - Yuka Sameshima-Yamashita
- Research Fellow of the Japan Society for the Promotion of Science
- National Institute for Agro-Environmental Sciences (NIAES)
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22
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Song YP, Miao FP, Yin XL, Ji NY. Nitrogenous cyclonerane sesquiterpenes from an algicolous strain of Trichoderma asperellum. Org Chem Front 2019. [DOI: 10.1039/c9qo00942f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Eight new nitrogenous cyclonerance derivatives (1–8) including two unprecedented hydroxamic acids (1 and 2) with potent algicidal activity were characterized from the algicolous fungus Trichoderma asperellum.
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Affiliation(s)
- Yin-Ping Song
- Yantai Institute of Coastal Zone Research
- Center for Ocean Mega-Science
- Chinese Academy of Sciences
- Yantai 264003
- People's Republic of China
| | - Feng-Ping Miao
- Yantai Institute of Coastal Zone Research
- Center for Ocean Mega-Science
- Chinese Academy of Sciences
- Yantai 264003
- People's Republic of China
| | - Xiu-Li Yin
- Yantai Institute of Coastal Zone Research
- Center for Ocean Mega-Science
- Chinese Academy of Sciences
- Yantai 264003
- People's Republic of China
| | - Nai-Yun Ji
- Yantai Institute of Coastal Zone Research
- Center for Ocean Mega-Science
- Chinese Academy of Sciences
- Yantai 264003
- People's Republic of China
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23
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Mukherjee PK, Hurley JF, Taylor JT, Puckhaber L, Lehner S, Druzhinina I, Schumacher R, Kenerley CM. Ferricrocin, the intracellular siderophore of Trichoderma virens, is involved in growth, conidiation, gliotoxin biosynthesis and induction of systemic resistance in maize. Biochem Biophys Res Commun 2018; 505:606-611. [PMID: 30278887 DOI: 10.1016/j.bbrc.2018.09.170] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 09/26/2018] [Indexed: 02/03/2023]
Abstract
Fungal siderophores are known to be involved in iron acquisition and storage, as well as pathogenicity of mammals and plants. As avirulent plant symbionts, Trichoderma spp. colonize roots and induce resistance responses both locally and systemically. To study the role of intracellular siderophore(s) in Trichoderma-plant interactions, we have obtained mutants in a non-ribosomal peptide synthetase, TvTex10, that was predicted to be involved in intracellular siderophore(s) biosynthesis. This gene has a detectable basal level of expression and is also upregulated under iron-deplete conditions. This is unlike two other siderophore-encoding genes, which are tightly regulated by iron. Disruption of tex10 gene using homologous recombination resulted in mutants with enhanced growth rate, reduced conidiation and hyper-sensitivity to oxidative stress as compared to wildtype strain. The mutants also produced reduced levels of gliotoxin and dimethyl gliotoxin but have enhanced ability to colonize maize seedling roots. The mutants were also impaired in induction of induced systemic resistance (ISR) in maize against the foliar pathogen Cochliobolus heterostrophus.
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Affiliation(s)
- Prasun K Mukherjee
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77840, USA; Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - James F Hurley
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77840, USA
| | - James T Taylor
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77840, USA
| | - Lorraine Puckhaber
- USDA ARS, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - Sylvia Lehner
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060, Vienna, Austria
| | - Irina Druzhinina
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060, Vienna, Austria
| | - Rainer Schumacher
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Charles M Kenerley
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77840, USA.
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24
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Fanelli F, Liuzzi VC, Logrieco AF, Altomare C. Genomic characterization of Trichoderma atrobrunneum (T. harzianum species complex) ITEM 908: insight into the genetic endowment of a multi-target biocontrol strain. BMC Genomics 2018; 19:662. [PMID: 30200883 PMCID: PMC6131884 DOI: 10.1186/s12864-018-5049-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND So far, biocontrol agent selection has been performed mainly by time consuming in vitro confrontation tests followed by extensive trials in greenhouse and field. An alternative approach is offered by application of high-throughput techniques, which allow extensive screening and comparison among strains for desired genetic traits. In the genus Trichoderma, the past assignments of particular features or strains to one species need to be reconsidered according to the recent taxonomic revisions. Here we present the genome of a biocontrol strain formerly known as Trichoderma harzianum ITEM 908, which exhibits both growth promoting capabilities and antagonism against different fungal pathogens, including Fusarium graminearum, Rhizoctonia solani, and the root-knot nematode Meloidogyne incognita. By genomic analysis of ITEM 908 we investigated the occurrence and the relevance of genes associated to biocontrol and stress tolerance, providing a basis for future investigation aiming to unravel the complex relationships between genomic endowment and exhibited activities of this strain. RESULTS The MLST analysis of ITS-TEF1 concatenated datasets reclassified ITEM 908 as T. atrobrunneum, a species recently described within the T. harzianum species complex and phylogenetically close to T. afroharzianum and T. guizhouense. Genomic analysis revealed the presence of a broad range of genes encoding for carbohydrate active enzymes (CAZYmes), proteins involved in secondary metabolites production, peptaboils, epidithiodioxopiperazines and siderophores potentially involved in parasitism, saprophytic degradation as well as in biocontrol and antagonistic activities. This abundance is comparable to other Trichoderma spp. in the T. harzianum species complex, but broader than in other biocontrol species and in the species T. reesei, known for its industrial application in cellulase production. Comparative analysis also demonstrated similar genomic organization of major secondary metabolites clusters, as in other Trichoderma species. CONCLUSIONS Reported data provide a contribution to a deeper understanding of the mode of action and identification of activity-specific genetic markers useful for selection and improvement of biocontrol strains. This work will also enlarge the availability of genomic data to perform comparative studies with the aim to correlate phenotypic differences with genetic diversity of Trichoderma species.
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Affiliation(s)
- Francesca Fanelli
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Vania Cosma Liuzzi
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | | | - Claudio Altomare
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
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25
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Montes-Bayón M, Sharar M, Corte-Rodriguez M. Trends on (elemental and molecular) mass spectrometry based strategies for speciation and metallomics. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2017.09.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Bignell E, Cairns TC, Throckmorton K, Nierman WC, Keller NP. Secondary metabolite arsenal of an opportunistic pathogenic fungus. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0023. [PMID: 28080993 DOI: 10.1098/rstb.2016.0023] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2016] [Indexed: 12/31/2022] Open
Abstract
Aspergillus fumigatus is a versatile fungus able to successfully exploit diverse environments from mammalian lungs to agricultural waste products. Among its many fitness attributes are dozens of genetic loci containing biosynthetic gene clusters (BGCs) producing bioactive small molecules (often referred to as secondary metabolites or natural products) that provide growth advantages to the fungus dependent on environment. Here we summarize the current knowledge of these BGCs-18 of which can be named to product-their expression profiles in vivo, and which BGCs may enhance virulence of this opportunistic human pathogen. Furthermore, we find extensive evidence for the presence of many of these BGCs, or similar BGCs, in distantly related genera including the emerging pathogen Pseudogymnoascus destructans, the causative agent of white-nose syndrome in bats, and suggest such BGCs may be predictive of pathogenic potential in other fungi.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Elaine Bignell
- Manchester Fungal Infection Group, Institute of Inflammation and Repair, 2.24 Core Technology Facility, Grafton Street, Manchester, M13 9NT, UK
| | - Timothy C Cairns
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Kurt Throckmorton
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
| | | | - Nancy P Keller
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA, .,Department of Medical Microbiology, University of Wisconsin, Madison, WI 53706, USA
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27
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Novák J, Sokolová L, Lemr K, Pluháček T, Palyzová A, Havlíček V. Batch-processing of imaging or liquid-chromatography mass spectrometry datasets and De Novo sequencing of polyketide siderophores. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:768-775. [PMID: 27956353 DOI: 10.1016/j.bbapap.2016.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 12/02/2016] [Accepted: 12/08/2016] [Indexed: 11/18/2022]
Abstract
The open-source and cross-platform software CycloBranch was utilized for dereplication of organic compounds from mass spectrometry imaging imzML datasets and its functions were illustrated on microbial siderophores. The pixel-to-pixel batch-processing was analogous to liquid chromatography mass spectrometry data. Each data point represented here by accurate m/z values and the corresponding ion intensities was matched against integrated compound libraries. The fine isotopic structure matching was also embedded into CycloBranch dereplication process. The siderophores' characterization from single-pixel mass spectra was further supported by their de novo sequencing. New ketide building block library was utilized by CycloBranch to characterize the siderophores in images and mixtures and nomenclature of fragment ion series of linear and cyclic polyketide siderophores was proposed. The software is freely available at http://ms.biomed.cas.cz/cyclobranch. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Jiří Novák
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Lucie Sokolová
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Karel Lemr
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Tomáš Pluháček
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Andrea Palyzová
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Vladimír Havlíček
- Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic.
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28
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Angel LPL, Yusof MT, Ismail IS, Ping BTY, Mohamed Azni INA, Kamarudin NH, Sundram S. An in vitro study of the antifungal activity of Trichoderma virens 7b and a profile of its non-polar antifungal components released against Ganoderma boninense. J Microbiol 2016; 54:732-744. [PMID: 27796927 DOI: 10.1007/s12275-016-6304-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 11/29/2022]
Abstract
Ganoderma boninense is the causal agent of a devastating disease affecting oil palm in Southeast Asian countries. Basal stem rot (BSR) disease slowly rots the base of palms, which radically reduces productive lifespan of this lucrative crop. Previous reports have indicated the successful use of Trichoderma as biological control agent (BCA) against G. boninense and isolate T. virens 7b was selected based on its initial screening. This study attempts to decipher the mechanisms responsible for the inhibition of G. boninense by identifying and characterizing the chemical compounds as well as the physical mechanisms by T. virens 7b. Hexane extract of the isolate gave 62.60% ± 6.41 inhibition against G. boninense and observation under scanning electron microscope (SEM) detected severe mycelial deformation of the pathogen at the region of inhibition. Similar mycelia deformation of G. boninense was observed with a fungicide treatment, Benlate® indicating comparable fungicidal effect by T. virens 7b. Fraction 4 and 5 of hexane active fractions through preparative thin layer chromatography (P-TLC) was identified giving the best inhibition of the pathogen. These fractions comprised of ketones, alcohols, aldehydes, lactones, sesquiterpenes, monoterpenes, sulphides, and free fatty acids profiled through gas chromatography mass spectrometry detector (GC/MSD). A novel antifungal compound discovery of phenylethyl alcohol (PEA) by T. virens 7b is reported through this study. T. virens 7b also proved to be an active siderophore producer through chrome azurol S (CAS) agar assay. The study demonstrated the possible mechanisms involved and responsible in the successful inhibition of G. boninense.
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Affiliation(s)
- Lee Pei Lee Angel
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia.,Biology Research Division, Malaysian Palm Oil Board, 43000, Kajang, Selangor, Malaysia
| | - Mohd Termizi Yusof
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Intan Safinar Ismail
- Department of Chemistry, Faculty of Science; Laboratory of Natural Products, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia.,Institute of Bioscience, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Bonnie Tay Yen Ping
- Advanced Oleochemical Technology Division, Malaysian Palm Oil Board, 43000, Kajang, Selangor, Malaysia
| | | | - Norman Hj Kamarudin
- Biology Research Division, Malaysian Palm Oil Board, 43000, Kajang, Selangor, Malaysia
| | - Shamala Sundram
- Biology Research Division, Malaysian Palm Oil Board, 43000, Kajang, Selangor, Malaysia.
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29
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Zeilinger S, Gruber S, Bansal R, Mukherjee PK. Secondary metabolism in Trichoderma – Chemistry meets genomics. FUNGAL BIOL REV 2016. [DOI: 10.1016/j.fbr.2016.05.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Tsednee M, Huang YC, Chen YR, Yeh KC. Identification of metal species by ESI-MS/MS through release of free metals from the corresponding metal-ligand complexes. Sci Rep 2016; 6:26785. [PMID: 27240899 PMCID: PMC4886218 DOI: 10.1038/srep26785] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 05/09/2016] [Indexed: 01/06/2023] Open
Abstract
Electrospray ionization-mass spectrometry (ESI-MS) is used to analyze metal species in a variety of samples. Here, we describe an application for identifying metal species by tandem mass spectrometry (ESI-MS/MS) with the release of free metals from the corresponding metal-ligand complexes. The MS/MS data were used to elucidate the possible fragmentation pathways of different metal-deoxymugineic acid (-DMA) and metal-nicotianamine (-NA) complexes and select the product ions with highest abundance that may be useful for quantitative multiple reaction monitoring. This method can be used for identifying different metal-ligand complexes, especially for metal species whose mass spectra peaks are clustered close together. Different metal-DMA/NA complexes were simultaneously identified under different physiological pH conditions with this method. We further demonstrated the application of the technique for different plant samples and with different MS instruments.
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Affiliation(s)
- Munkhtsetseg Tsednee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Yu-Chen Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Kuo-Chen Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529 Taiwan
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Saha M, Sarkar S, Sarkar B, Sharma BK, Bhattacharjee S, Tribedi P. Microbial siderophores and their potential applications: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:3984-99. [PMID: 25758420 DOI: 10.1007/s11356-015-4294-0] [Citation(s) in RCA: 298] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/27/2015] [Indexed: 05/18/2023]
Abstract
Siderophores are small organic molecules produced by microorganisms under iron-limiting conditions which enhance the uptake of iron to the microorganisms. In environment, the ferric form of iron is insoluble and inaccessible at physiological pH (7.35-7.40). Under this condition, microorganisms synthesize siderophores which have high affinity for ferric iron. These ferric iron-siderophore complexes are then transported to cytosol. In cytosol, the ferric iron gets reduced into ferrous iron and becomes accessible to microorganism. In recent times, siderophores have drawn much attention due to its potential roles in different fields. Siderophores have application in microbial ecology to enhance the growth of several unculturable microorganisms and can alter the microbial communities. In the field of agriculture, different types of siderophores promote the growth of several plant species and increase their yield by enhancing the Fe uptake to plants. Siderophores acts as a potential biocontrol agent against harmful phyto-pathogens and holds the ability to substitute hazardous pesticides. Heavy-metal-contaminated samples can be detoxified by applying siderophores, which explicate its role in bioremediation. Siderophores can detect the iron content in different environments, exhibiting its role as a biosensor. In the medical field, siderophore uses the "Trojan horse strategy" to form complexes with antibiotics and helps in the selective delivery of antibiotics to the antibiotic-resistant bacteria. Certain iron overload diseases for example sickle cell anemia can be treated with the help of siderophores. Other medical applications of siderophores include antimalarial activity, removal of transuranic elements from the body, and anticancer activity. The aim of this review is to discuss the important roles and applications of siderophores in different sectors including ecology, agriculture, bioremediation, biosensor, and medicine.
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Affiliation(s)
- Maumita Saha
- Department of Molecular Biology & Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura, 799022, India
| | - Subhasis Sarkar
- Department of Molecular Biology & Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura, 799022, India
| | - Biplab Sarkar
- National Institute of Abiotic Stress Management, Baramati, 413115, Pune, Maharashtra, India
| | - Bipin Kumar Sharma
- Department of Microbiology, Tripura University (A Central University), Suryamaninagar, Tripura, 799022, India
| | - Surajit Bhattacharjee
- Department of Molecular Biology & Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura, 799022, India.
| | - Prosun Tribedi
- Department of Microbiology, Tripura University (A Central University), Suryamaninagar, Tripura, 799022, India.
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Pluháček T, Lemr K, Ghosh D, Milde D, Novák J, Havlíček V. Characterization of microbial siderophores by mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:35-47. [PMID: 25980644 DOI: 10.1002/mas.21461] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/19/2014] [Indexed: 05/28/2023]
Abstract
Siderophores play important roles in microbial iron piracy, and are applied as infectious disease biomarkers and novel pharmaceutical drugs. Inductively coupled plasma and molecular mass spectrometry (ICP-MS) combined with high resolution separations allow characterization of siderophores in complex samples taking advantages of mass defect data filtering, tandem mass spectrometry, and iron-containing compound quantitation. The enrichment approaches used in siderophore analysis and current ICP-MS technologies are reviewed. The recent tools for fast dereplication of secondary metabolites and their databases are reported. This review on siderophores is concluded with their recent medical, biochemical, geochemical, and agricultural applications in mass spectrometry context.
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Affiliation(s)
- Tomáš Pluháček
- Department of Analytical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky University, 17. listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Microbiology, AS CR v.v.i., Videnska 1083, CZ 142 20, Prague 4, Czech Republic
| | - Karel Lemr
- Department of Analytical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky University, 17. listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Microbiology, AS CR v.v.i., Videnska 1083, CZ 142 20, Prague 4, Czech Republic
| | - Dipankar Ghosh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - David Milde
- Department of Analytical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky University, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Novák
- Institute of Microbiology, AS CR v.v.i., Videnska 1083, CZ 142 20, Prague 4, Czech Republic
| | - Vladimír Havlíček
- Department of Analytical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky University, 17. listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Microbiology, AS CR v.v.i., Videnska 1083, CZ 142 20, Prague 4, Czech Republic
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Druzhinina IS, Kubicek CP. Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:69-147. [PMID: 27261782 DOI: 10.1016/bs.aambs.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.
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Affiliation(s)
- I S Druzhinina
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - C P Kubicek
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
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Baars O, Zhang X, Morel FMM, Seyedsayamdost MR. The Siderophore Metabolome of Azotobacter vinelandii. Appl Environ Microbiol 2016; 82:27-39. [PMID: 26452553 PMCID: PMC4702634 DOI: 10.1128/aem.03160-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/02/2015] [Indexed: 12/14/2022] Open
Abstract
In this study, we performed a detailed characterization of the siderophore metabolome, or "chelome," of the agriculturally important and widely studied model organism Azotobacter vinelandii. Using a new high-resolution liquid chromatography-mass spectrometry (LC-MS) approach, we found over 35 metal-binding secondary metabolites, indicative of a vast chelome in A. vinelandii. These include vibrioferrin, a siderophore previously observed only in marine bacteria. Quantitative analyses of siderophore production during diazotrophic growth with different sources and availabilities of Fe showed that, under all tested conditions, vibrioferrin was present at the highest concentration of all siderophores and suggested new roles for vibrioferrin in the soil environment. Bioinformatic searches confirmed the capacity for vibrioferrin production in Azotobacter spp. and other bacteria spanning multiple phyla, habitats, and lifestyles. Moreover, our studies revealed a large number of previously unreported derivatives of all known A. vinelandii siderophores and rationalized their origins based on genomic analyses, with implications for siderophore diversity and evolution. Together, these insights provide clues as to why A. vinelandii harbors multiple siderophore biosynthesis gene clusters. Coupled with the growing evidence for alternative functions of siderophores, the vast chelome in A. vinelandii may be explained by multiple, disparate evolutionary pressures that act on siderophore production.
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Affiliation(s)
- Oliver Baars
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
| | - François M M Morel
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
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Bazafkan H, Dattenböck C, Böhmdorfer S, Tisch D, Stappler E, Schmoll M. Mating type-dependent partner sensing as mediated by VEL1 in Trichoderma reesei. Mol Microbiol 2015; 96:1103-18. [PMID: 25757597 PMCID: PMC4949666 DOI: 10.1111/mmi.12993] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2015] [Indexed: 12/21/2022]
Abstract
Sexual development in the filamentous model ascomycete Trichoderma reesei (syn. Hypocrea jecorina) was described only a few years ago. In this study, we show a novel role for VELVET in fungi, which links light response, development and secondary metabolism. Vel1 is required for mating in darkness, normal growth and conidiation. In light, vel1 was dispensable for male fertility but essential for female fertility in both mating types. VEL1 impacted regulation of the pheromone system (hpr1, hpr2, hpp1, ppg1) in a mating type‐dependent manner and depending on the mating partner of a given strain. These partner effects only occurred for hpp1 and hpr2, the pheromone precursor and receptor genes associated with the MAT1‐2 mating type and for the mating type gene mat1‐2‐1. Analysis of secondary metabolite patterns secreted by wild type and mutants under asexual and sexual conditions revealed that even in the wild type, the patterns change upon encounter of a mating partner, with again distinct differences for wild type and vel1 mutants. Hence, T. reesei applies a language of pheromones and secondary metabolites to communicate with mating partners and that this communication is at least in part mediated by VEL1.
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Affiliation(s)
- Hoda Bazafkan
- Department Health and Environment, AIT Austrian Institute of Technology GmbH, Bioresources, Konrad-Lorenz Strasse 24, Tulln, 3430, Austria
| | - Christoph Dattenböck
- Department Health and Environment, AIT Austrian Institute of Technology GmbH, Bioresources, Konrad-Lorenz Strasse 24, Tulln, 3430, Austria
| | - Stefan Böhmdorfer
- University of Natural Resources and Life Sciences Vienna, Department of Chemistry, Division of Chemistry of Renewable Resources, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
| | - Doris Tisch
- Research Area Molecular Biotechnology, Vienna University of Technology, Gumpendorfer Straße 1a, Wien, 1060, Austria
| | - Eva Stappler
- Department Health and Environment, AIT Austrian Institute of Technology GmbH, Bioresources, Konrad-Lorenz Strasse 24, Tulln, 3430, Austria
| | - Monika Schmoll
- Department Health and Environment, AIT Austrian Institute of Technology GmbH, Bioresources, Konrad-Lorenz Strasse 24, Tulln, 3430, Austria
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Boiteau RM, Repeta DJ. An extended siderophore suite from Synechococcus sp. PCC 7002 revealed by LC-ICPMS-ESIMS. Metallomics 2015; 7:877-84. [DOI: 10.1039/c5mt00005j] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
New members of the synechobactin siderophore suite with variable hydroxamate chain length were discovered using an LCMS based pipeline for the sensitive characterization of iron complexes.
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Affiliation(s)
- Rene M. Boiteau
- Department of Marine Chemistry and Geochemistry
- Woods Hole Oceanographic Institution
- Woods Hole, USA
- Department of Earth
- Atmospheric and Planetary Sciences
| | - Daniel J. Repeta
- Department of Marine Chemistry and Geochemistry
- Woods Hole Oceanographic Institution
- Woods Hole, USA
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37
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Daguerre Y, Siegel K, Edel-Hermann V, Steinberg C. Fungal proteins and genes associated with biocontrol mechanisms of soil-borne pathogens: a review. FUNGAL BIOL REV 2014. [DOI: 10.1016/j.fbr.2014.11.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Baars O, Morel FMM, Perlman DH. ChelomEx: Isotope-assisted discovery of metal chelates in complex media using high-resolution LC-MS. Anal Chem 2014; 86:11298-305. [PMID: 25333600 DOI: 10.1021/ac503000e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chelating agents can control the speciation and reactivity of trace metals in biological, environmental, and laboratory-derived media. A large number of trace metals (including Fe, Cu, Zn, Hg, and others) show characteristic isotopic fingerprints that can be exploited for the discovery of known and unknown organic metal complexes and related chelating ligands in very complex sample matrices using high-resolution liquid chromatography mass spectrometry (LC-MS). However, there is currently no free open-source software available for this purpose. We present a novel software tool, ChelomEx, which identifies isotope pattern-matched chromatographic features associated with metal complexes along with free ligands and other related adducts in high-resolution LC-MS data. High sensitivity and exclusion of false positives are achieved by evaluation of the chromatographic coherence of the isotope pattern within chromatographic features, which we demonstrate through the analysis of bacterial culture media. A built-in graphical user interface and compound library aid in identification and efficient evaluation of results. ChelomEx is implemented in MatLab. The source code, binaries for MS Windows and MAC OS X as well as test LC-MS data are available for download at SourceForge ( http://sourceforge.net/projects/chelomex ).
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Affiliation(s)
- Oliver Baars
- Department of Geosciences, Princeton University , Princeton, New Jersey 08544, United States
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Pourhassan N, Gagnon R, Wichard T, Bellenger JP. Identification of the Hydroxamate Siderophore Ferricrocin in Cladosporium cladosporioides. Nat Prod Commun 2014. [DOI: 10.1177/1934578x1400900429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The hydroxamate siderophore ferricrocin was identified in Cladosporium cladosporioides growth medium by solid phase extraction and ultra high pressure liquid chromatography coupled to a time of flight mass spectrometer (UHPLC/QTOF-MS). Both desferricrocin and ferricrocin were detected in the extracellular medium assisted by high resolution mass spectrometry. This is the first identification of a hydroxamate siderophore in Cladosporium cladosporioides. This finding emphasizes the common meaning of ferricrocin in fungi.
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Affiliation(s)
- Nina Pourhassan
- Département de Chimie, Université de Sherbrooke, 2500 Boul. de I'Université, Sherbrooke, Québec J1K2R1, Canada
| | - René Gagnon
- Département de Chimie, Université de Sherbrooke, 2500 Boul. de I'Université, Sherbrooke, Québec J1K2R1, Canada
| | - Thomas Wichard
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Lessingstr.8, 07743 Jena, Germany
| | - Jean-Philippe Bellenger
- Département de Chimie, Université de Sherbrooke, 2500 Boul. de I'Université, Sherbrooke, Québec J1K2R1, Canada
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Deicke M, Mohr JF, Bellenger JP, Wichard T. Metallophore mapping in complex matrices by metal isotope coded profiling of organic ligands. Analyst 2014; 139:6096-9. [DOI: 10.1039/c4an01461h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal isotope coded profiling (MICP) utilizes stable metal isotope pairs creating unique isotopic signatures used for fast identification of metallophores, metal ion buffers or sequestering agents.
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Affiliation(s)
- Michael Deicke
- Friedrich Schiller University Jena
- Institute for Inorganic and Analytical Chemistry
- 07743 Jena, Germany
| | - Jan Frieder Mohr
- Friedrich Schiller University Jena
- Institute for Inorganic and Analytical Chemistry
- 07743 Jena, Germany
| | | | - Thomas Wichard
- Friedrich Schiller University Jena
- Institute for Inorganic and Analytical Chemistry
- 07743 Jena, Germany
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Sørensen JL, Knudsen M, Hansen FT, Olesen C, Fuertes PR, Lee TV, Sondergaard TE, Pedersen CNS, Brodersen DE, Giese H. Fungal NRPS-Dependent Siderophores: From Function to Prediction. Fungal Biol 2014. [DOI: 10.1007/978-1-4939-1191-2_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Carroux A, Van Bohemen AI, Roullier C, Robiou du Pont T, Vansteelandt M, Bondon A, Zalouk-Vergnoux A, Pouchus YF, Ruiz N. Unprecedented 17-residue peptaibiotics produced by marine-derived Trichoderma atroviride. Chem Biodivers 2013; 10:772-86. [PMID: 23681725 DOI: 10.1002/cbdv.201200398] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Indexed: 11/07/2022]
Abstract
In the course of investigations on marine-derived toxigenic fungi, five strains of Trichoderma atroviride were studied for their production of peptaibiotics. While these five strains were found to produce classical 19-residue peptaibols, three of them exhibited unusual peptidic sodium-adduct [M + 2 Na](2+) ion peaks at m/z between 824 and 854. The sequencing of these peptides led to two series of unprecedented 17-residue peptaibiotics based on the model Ac-XXX-Ala-Ala-XXX-XXX-Gln-Aib-Aib-Aib-Ala/Ser-Lxx-Aib-Pro-XXX-Aib-Lxx-[C(129) ]. The C-terminus of these new peptides was common to all of them, and its elemental formula C5 H9 N2 O2 was established by HR-MS. It could correspond to the cyclized form of N(δ) -hydroxyornithine which has already been observed at the C-terminus of various peptidic siderophores. The comparison of the sequences of 17- and 19-residue peptides showed similarities for positions 1-16. This observation seems to indicate a common biosynthesis pathway. Both new 17-residue peptaibiotics and 19-residue peptaibols exhibited weak in vitro cytotoxicities against KB cells.
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Affiliation(s)
- Angélique Carroux
- University of Nantes, LUNAM, Faculty of Pharmacy, MMS, F-44000 Nantes
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Bischof R, Fourtis L, Limbeck A, Gamauf C, Seiboth B, Kubicek CP. Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:127. [PMID: 24016404 PMCID: PMC3847502 DOI: 10.1186/1754-6834-6-127] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/04/2013] [Indexed: 05/05/2023]
Abstract
BACKGROUND Renewable lignocellulosic biomass is an advantageous resource for the production of second generation biofuels and other biorefinery products. In Middle Europe, wheat straw is one of the most abundant low-cost sources of lignocellulosic biomass. For its efficient use, an efficient mix of cellulases and hemicellulases is required. In this paper, we investigated how cellulase production by T. reesei on wheat straw compares to that on lactose, the only soluble and also cheap inducing carbon source for enzyme production. RESULTS We have examined and compared the transcriptome of T. reesei growing on wheat straw and lactose as carbon sources under otherwise similar conditions. Gene expression on wheat straw exceeded that on lactose, and 1619 genes were found to be only induced on wheat straw but not on lactose. They comprised 30% of the CAZome, but were also enriched in genes associated with phospholipid metabolism, DNA synthesis and repair, iron homeostatis and autophagy. Two thirds of the CAZome was expressed both on wheat straw as well as on lactose, but 60% of it at least >2-fold higher on the former. Major wheat straw specific genes comprised xylanases, chitinases and mannosidases. Interestingly, the latter two CAZyme families were significantly higher expressed in a strain in which xyr1 encoding the major regulator of cellulase and hemicellulase biosynthesis is non-functional. CONCLUSIONS Our data reveal several major differences in the transcriptome between wheat straw and lactose which may be related to the higher enzyme formation on the former and their further investigation could lead to the development of methods for increasing enzyme production on lactose.
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Affiliation(s)
- Robert Bischof
- Austrian Centre of Industrial Biotechnology (ACIB) GmBH c/o Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
| | - Lukas Fourtis
- Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
| | - Andreas Limbeck
- Institute of Chemical Technologies and Analytics, University of Technology of Vienna, Getreidemarkt 9, Vienna A-1060, Austria
| | - Christian Gamauf
- Biotech & Renewables Center, Clariant GmbH, München 81477, Germany
| | - Bernhard Seiboth
- Austrian Centre of Industrial Biotechnology (ACIB) GmBH c/o Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
- Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
| | - Christian P Kubicek
- Austrian Centre of Industrial Biotechnology (ACIB) GmBH c/o Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
- Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
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Mukherjee PK, Horwitz BA, Herrera-Estrella A, Schmoll M, Kenerley CM. Trichoderma research in the genome era. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:105-29. [PMID: 23915132 DOI: 10.1146/annurev-phyto-082712-102353] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Trichoderma species are widely used in agriculture and industry as biopesticides and sources of enzymes, respectively. These fungi reproduce asexually by production of conidia and chlamydospores and in wild habitats by ascospores. Trichoderma species are efficient mycoparasites and prolific producers of secondary metabolites, some of which have clinical importance. However, the ecological or biological significance of this metabolite diversity is sorely lagging behind the chemical significance. Many strains produce elicitors and induce resistance in plants through colonization of roots. Seven species have now been sequenced. Comparison of a primarily saprophytic species with two mycoparasitic species has provided striking contrasts and has established that mycoparasitism is an ancestral trait of this genus. Among the interesting outcomes of genome comparison is the discovery of a vast repertoire of secondary metabolism pathways and of numerous small cysteine-rich secreted proteins. Genomics has also facilitated investigation of sexual crossing in Trichoderma reesei, suggesting the possibility of strain improvement through hybridization.
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Affiliation(s)
- Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Center, Trombay, Mumbai 400085, India.
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