1
|
Maini Rekdal V, Villalobos-Escobedo JM, Rodriguez-Valeron N, Olaizola Garcia M, Prado Vásquez D, Rosales A, Sörensen PM, Baidoo EEK, Calheiros de Carvalho A, Riley R, Lipzen A, He G, Yan M, Haridas S, Daum C, Yoshinaga Y, Ng V, Grigoriev IV, Munk R, Wijaya CH, Nuraida L, Damayanti I, Cruz-Morales P, Keasling JD. Neurospora intermedia from a traditional fermented food enables waste-to-food conversion. Nat Microbiol 2024:10.1038/s41564-024-01799-3. [PMID: 39209985 DOI: 10.1038/s41564-024-01799-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
Fungal fermentation of food and agricultural by-products holds promise for improving food sustainability and security. However, the molecular basis of fungal waste-to-food upcycling remains poorly understood. Here we use a multi-omics approach to characterize oncom, a fermented food traditionally produced from soymilk by-products in Java, Indonesia. Metagenomic sequencing of samples from small-scale producers in Western Java indicated that the fungus Neurospora intermedia dominates oncom. Further transcriptomic, metabolomic and phylogenomic analysis revealed that oncom-derived N. intermedia utilizes pectin and cellulose degradation during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. Finally, we found that N. intermedia grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and could create foods that were positively perceived by consumers outside Indonesia. These results showcase the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products.
Collapse
Affiliation(s)
- Vayu Maini Rekdal
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- Miller Institute for Basic Research in Science, University of California Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - José Manuel Villalobos-Escobedo
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Tecnológico de Monterrey, Institute for Obesity Research, Monterrey, Nuevo León, Mexico
| | - Nabila Rodriguez-Valeron
- ALCHEMIST Explore, Research and Development, Alchemist Aps, Copenhagen, Denmark
- Basque Culinary Center, Mondragon Universitatea, Donostia, Gipuzkoa, Spain
| | | | - Diego Prado Vásquez
- ALCHEMIST Explore, Research and Development, Alchemist Aps, Copenhagen, Denmark
| | - Alexander Rosales
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Pia M Sörensen
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ana Calheiros de Carvalho
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rasmus Munk
- ALCHEMIST Explore, Research and Development, Alchemist Aps, Copenhagen, Denmark
| | - Christofora Hanny Wijaya
- Department of Food Science and Technology, Faculty of Agricultural Engineering, IPB University (Bogor Agricultural University), Dramaga, Indonesia
| | - Lilis Nuraida
- Department of Food Science and Technology, Faculty of Agricultural Engineering, IPB University (Bogor Agricultural University), Dramaga, Indonesia
| | - Isty Damayanti
- Department of Food Science and Technology, Faculty of Agricultural Engineering, IPB University (Bogor Agricultural University), Dramaga, Indonesia
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
- California Institute of Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA.
| |
Collapse
|
2
|
Chatrath A, Dey P, Greeley K, Maciel G, Huang L, Heiss C, Black I, Azadi P, Free SJ. Characterization of the Neurospora crassa Galactosaminogalactan Biosynthetic Pathway. Microorganisms 2024; 12:1509. [PMID: 39203353 PMCID: PMC11356417 DOI: 10.3390/microorganisms12081509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 09/03/2024] Open
Abstract
The Neurospora crassa genome has a gene cluster for the synthesis of galactosaminogalactan (GAG). The gene cluster includes the following: (1) UDP-glucose-4-epimerase to convert UDP-glucose and UDP-N-acetylglucosamine to UDP-galactose and UDP-N-acetylgalactosamine (NCU05133), (2) GAG synthase for the synthesis of an acetylated GAG (NCU05132), (3) GAG deacetylase (/NCW-1/NCU05137), (4) GH135-1, a GAG hydrolase with specificity for N-acetylgalactosamine-containing GAG (NCU05135), and (5) GH114-1, a galactosaminidase with specificity for galactosamine-containing GAG (NCU05136). The deacetylase was previously shown to be a major cell wall glycoprotein and given the name of NCW-1 (non-GPI anchored cell wall protein-1). Characterization of the polysaccharides found in the growth medium from the wild type and the GAG synthase mutant demonstrates that there is a major reduction in the levels of polysaccharides containing galactosamine and N-acetylgalactosamine in the mutant growth medium, providing evidence that the synthase is responsible for the production of a GAG. The analysis also indicates that there are other galactose-containing polysaccharides produced by the fungus. Phenotypic characterization of wild-type and mutant isolates showed that deacetylated GAG from the wild type can function as an adhesin to a glass surface and provides the fungal mat with tensile strength, demonstrating that the deacetylated GAG functions as an intercellular adhesive. The acetylated GAG produced by the deacetylase mutant was found to function as an adhesive for chitin, alumina, celite (diatomaceous earth), activated charcoal, and wheat leaf particulates.
Collapse
Affiliation(s)
- Apurva Chatrath
- Department of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, USA; (A.C.); (K.G.)
| | - Protyusha Dey
- Department of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, USA; (A.C.); (K.G.)
| | - Kevin Greeley
- Department of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, USA; (A.C.); (K.G.)
| | - Gabriela Maciel
- Department of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, USA; (A.C.); (K.G.)
| | - Lei Huang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (L.H.)
| | - Christian Heiss
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (L.H.)
| | - Ian Black
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (L.H.)
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (L.H.)
| | - Stephen J. Free
- Department of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, USA; (A.C.); (K.G.)
| |
Collapse
|
3
|
Kollath-Leiß K, Repnik U, Winter H, Winkelmann H, Freund AS, Kempken F. The First Observation of the Filamentous Fungus Neurospora crassa Growing in the Roots of the Grass Brachypodium distachyon. J Fungi (Basel) 2024; 10:487. [PMID: 39057371 PMCID: PMC11278470 DOI: 10.3390/jof10070487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
The model organism Neurospora crassa has been cultivated in laboratories since the 1920s and its saprotrophic lifestyle has been established for decades. However, beyond their role as saprotrophs, fungi engage in intricate relationships with plants, showcasing diverse connections ranging from mutualistic to pathogenic. Although N. crassa has been extensively investigated under laboratory conditions, its ecological characteristics remain largely unknown. In contrast, Brachypodium distachyon, a sweet grass closely related to significant crops, demonstrates remarkable ecological flexibility and participates in a variety of fungal interactions, encompassing both mutualistic and harmful associations. Through a comprehensive microscopic analysis using electron, fluorescence, and confocal laser scanning microscopy, we discovered a novel endophytic interaction between N. crassa and B. distachyon roots, where fungal hyphae not only thrive in the apoplastic space and vascular bundle but also may colonize plant root cells. This new and so far hidden trait of one of the most important fungal model organisms greatly enhances our view of N. crassa, opening new perspectives concerning the fungus' ecological role. In addition, we present a new tool for studying plant-fungus interspecies communication, combining two well-established model systems, which improves our possibilities of experimental design on the molecular level.
Collapse
Affiliation(s)
- Krisztina Kollath-Leiß
- Abt. für Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität, 24098 Kiel, Germany; (H.W.); (A.S.F.)
| | - Urska Repnik
- Zentrale Mikroskopie, Christian-Albrechts-Universität, 24118 Kiel, Germany;
| | - Hannes Winter
- Abt. für Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität, 24098 Kiel, Germany; (H.W.); (A.S.F.)
| | - Heinrich Winkelmann
- Abt. für Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität, 24098 Kiel, Germany; (H.W.); (A.S.F.)
| | - Anna Sophia Freund
- Abt. für Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität, 24098 Kiel, Germany; (H.W.); (A.S.F.)
| | - Frank Kempken
- Abt. für Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität, 24098 Kiel, Germany; (H.W.); (A.S.F.)
| |
Collapse
|
4
|
Rungjindamai N, Jones EBG. Why Are There So Few Basidiomycota and Basal Fungi as Endophytes? A Review. J Fungi (Basel) 2024; 10:67. [PMID: 38248976 PMCID: PMC10820240 DOI: 10.3390/jof10010067] [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: 11/29/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
A review of selected studies on fungal endophytes confirms the paucity of Basidiomycota and basal fungi, with almost 90% attributed to Ascomycota. Reasons for the low number of Basidiomycota and basal fungi, including the Chytridiomycota, Mucoromycota, and Mortierellomycota, are advanced, including isolation procedure and media, incubation period and the slow growth of basidiomycetes, the identification of non-sporulating isolates, endophyte competition, and fungus-host interactions. We compare the detection of endophytes through culture-dependent methods and culture-independent methods, the role of fungi on senescence of the host plant, and next-generation studies.
Collapse
Affiliation(s)
- Nattawut Rungjindamai
- Department of Biology, School of Science, King Mongkut’s Institute of Technology Ladkrabang (KMITL), Chalongkrung Road, Ladkrabang, Bangkok 10520, Thailand
| | - E. B. Gareth Jones
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| |
Collapse
|
5
|
Waqar S, Bhat AA, Khan AA. Endophytic fungi: Unravelling plant-endophyte interaction and the multifaceted role of fungal endophytes in stress amelioration. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108174. [PMID: 38070242 DOI: 10.1016/j.plaphy.2023.108174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 02/15/2024]
Abstract
Endophytic fungi colonize interior plant tissue and mostly form mutualistic associations with their host plant. Plant-endophyte interaction is a complex mechanism and is currently a focus of research to understand the underlying mechanism of endophyte asymptomatic colonization, the process of evading plant immune response, modulation of gene expression, and establishment of a balanced mutualistic relationship. Fungal endophytes rely on plant hosts for nutrients, shelter, and transmission and improve the host plant's tolerance against biotic stresses, including -herbivores, nematodes, bacterial, fungal, viral, nematode, and other phytopathogens. Endophytic fungi have been reported to improve plant health by reducing and eradicating the harmful effect of phytopathogens through competition for space or nutrients, mycoparasitism, and through direct or indirect defense systems by producing secondary metabolites as well as by induced systemic resistance (ISR). Additionally, for efficient crop improvement, practicing them would be a fruitful step for a sustainable approach. This review article summarizes the current research progress in plant-endophyte interaction and the fungal endophyte mechanism to overcome host defense responses, their subsequent colonization, and the establishment of a balanced mutualistic interaction with host plants. This review also highlighted the potential of fungal endophytes in the amelioration of biotic stress. We have also discussed the relevance of various bioactive compounds possessing antimicrobial potential against a variety of agricultural pathogens. Furthermore, endophyte-mediated ISR is also emphasized.
Collapse
Affiliation(s)
- Sonia Waqar
- Section of Environmental Botany and Plant Pathology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.
| | - Adil Ameen Bhat
- Section of Environmental Botany and Plant Pathology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.
| | - Abrar Ahmad Khan
- Section of Environmental Botany and Plant Pathology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.
| |
Collapse
|
6
|
McLaughlin MS, Roy M, Abbasi PA, Carisse O, Yurgel SN, Ali S. Why Do We Need Alternative Methods for Fungal Disease Management in Plants? PLANTS (BASEL, SWITZERLAND) 2023; 12:3822. [PMID: 38005718 PMCID: PMC10675458 DOI: 10.3390/plants12223822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
Fungal pathogens pose a major threat to food production worldwide. Traditionally, chemical fungicides have been the primary means of controlling these pathogens, but many of these fungicides have recently come under increased scrutiny due to their negative effects on the health of humans, animals, and the environment. Furthermore, the use of chemical fungicides can result in the development of resistance in populations of phytopathogenic fungi. Therefore, new environmentally friendly alternatives that provide adequate levels of disease control are needed to replace chemical fungicides-if not completely, then at least partially. A number of alternatives to conventional chemical fungicides have been developed, including plant defence elicitors (PDEs); biological control agents (fungi, bacteria, and mycoviruses), either alone or as consortia; biochemical fungicides; natural products; RNA interference (RNAi) methods; and resistance breeding. This article reviews the conventional and alternative methods available to manage fungal pathogens, discusses their strengths and weaknesses, and identifies potential areas for future research.
Collapse
Affiliation(s)
- Michael S. McLaughlin
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 4H5, Canada
| | - Maria Roy
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | - Pervaiz A. Abbasi
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
| | - Odile Carisse
- Saint-Jean-sur-Richelieu Research Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 7B5, Canada;
| | - Svetlana N. Yurgel
- United States Department of Agriculture (USDA), Agricultural Research Service, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA;
| | - Shawkat Ali
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
| |
Collapse
|
7
|
Dort EN, Layne E, Feau N, Butyaev A, Henrissat B, Martin FM, Haridas S, Salamov A, Grigoriev IV, Blanchette M, Hamelin RC. Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits. Sci Rep 2023; 13:17203. [PMID: 37821494 PMCID: PMC10567782 DOI: 10.1038/s41598-023-44005-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.
Collapse
Affiliation(s)
- E N Dort
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - E Layne
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - N Feau
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | - A Butyaev
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - B Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - F M Martin
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Université de Lorraine, Champenoux, France
| | - S Haridas
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - A Salamov
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - I V Grigoriev
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - M Blanchette
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - R C Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, QC, Canada.
| |
Collapse
|
8
|
Patil R, Ajagunde J, Khan S, Kannuri S, Gandham N, Mukhida S. Rhino-orbital cerebral mycosis: a case series of non-mucorales in COVID patients. Access Microbiol 2023; 5:000575.v4. [PMID: 37970091 PMCID: PMC10634496 DOI: 10.1099/acmi.0.000575.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/18/2023] [Indexed: 11/17/2023] Open
Abstract
Introduction Rhino-Orbito-cerebral mycoses are not only caused by Aspergillus spp. and Zygomycetes spp. but also can be associated with other rare species such as Neurospora spp., Cladosporium spp. and Fusarium spp. Mucormycosis is associated causatively with immunocompromised states, for example patients with comorbidities such as diabetes mellitus. Clinical symptoms of coronavirus disease (COVID) and mucormycosis in tandem are critical and relentless, frequently with no life-saving treatment. Case series We report three patients with COVID-19 infection, who during the course of treatment developed rhino-orbital-cerebral mycosis including oral cavity involvement. Rhinocerebral mycosis along with oral cavity involvement was diagnosed by radiological investigations and preliminary screening for fungal infection (KOH mount) in all three cases. Empirical treatment was started but patients did not respond to treatment. All patients died even after debridement and maxillectomy. On culture, rare species of fungi were isolated in all three cases which, with the help of a reference laboratory, were identified as Neurospora, Cladosporium and Fusarium. Neurospora is considered nonpathogenic to humans. Cladosporium is a dematiaceous fungus found in soil in all climates, associated with disseminated or cerebral infections; and Fusarium, though considered a saprophytic colonizer of skin and respiratory mucosa along with other bacteria, is a common cause of mycotic keratitis worldwide. Conclusion Immune system modifications due to COVID-19 with/without other risk factors can result in fungal co-infections that prove to be fatal for the patients. It is vital to be aware that COVID-19 patients, particularly those who are critically ill, may acquire secondary fungal infections and early detection is critical.
Collapse
Affiliation(s)
- Rajashri Patil
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, Maharashtra, India
| | - Jyoti Ajagunde
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, Maharashtra, India
| | - Sameena Khan
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, Maharashtra, India
| | - Sriram Kannuri
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, Maharashtra, India
| | - Nageswari Gandham
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, Maharashtra, India
| | - Sahjid Mukhida
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, Maharashtra, India
| |
Collapse
|
9
|
Greenwood L, Nimmo DG, Egidi E, Price JN, McIntosh R, Frew A. Fire shapes fungal guild diversity and composition through direct and indirect pathways. Mol Ecol 2023; 32:4921-4939. [PMID: 37452603 DOI: 10.1111/mec.17068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Fire has shaped global ecosystems for millennia by directly killing organisms and indirectly altering habitats and resources. All terrestrial ecosystems, including fire-prone ecosystems, rely on soil-inhabiting fungi, where they play vital roles in ecological processes. Yet our understanding of how fire regimes influence soil fungi remains limited and our knowledge of these interactions in semiarid landscapes is virtually absent. We collected soil samples and vegetation measurements from sites across a gradient in time-since-fire ages (0-75 years-since-fire) and fire frequency (burnt 0-5 times during the recent 29-year period) in a semiarid heathland of south-eastern Australia. We characterized fungal communities using ITS amplicon-sequencing and assigned fungi taxonomically to trophic guilds. We used structural equation models to examine direct, indirect and total effects of time-since-fire and fire frequency on total fungal, ectomycorrhizal, saprotrophic and pathogenic richness. We used multivariate analyses to investigate how total fungal, ectomycorrhizal, saprotrophic and pathogenic species composition differed between post-fire successional stages and fire frequency classes. Time-since-fire was an important driver of saprotrophic richness; directly, saprotrophic richness increased with time-since-fire, and indirectly, saprotrophic richness declined with time-since-fire (resulting in a positive total effect), mediated through the impact of fire on substrates. Frequently burnt sites had lower numbers of saprotrophic and pathogenic species. Post-fire successional stages and fire frequency classes were characterized by distinct fungal communities, with large differences in ectomycorrhizal species composition. Understanding the complex responses of fungal communities to fire can be improved by exploring how the effects of fire flow through ecosystems. Diverse fire histories may be important for maintaining the functional diversity of fungi in semiarid regions.
Collapse
Affiliation(s)
- Leanne Greenwood
- Gulbali Institute, Charles Sturt University, Thurgoona, New South Wales, Australia
| | - Dale G Nimmo
- Gulbali Institute, Charles Sturt University, Thurgoona, New South Wales, Australia
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Jodi N Price
- Gulbali Institute, Charles Sturt University, Thurgoona, New South Wales, Australia
| | | | - Adam Frew
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| |
Collapse
|
10
|
Bell-Dereske LP, Benucci GMN, da Costa PB, Bonito G, Friesen ML, Tiemann LK, Evans SE. Regional biogeography versus intra-annual dynamics of the root and soil microbiome. ENVIRONMENTAL MICROBIOME 2023; 18:50. [PMID: 37287059 DOI: 10.1186/s40793-023-00504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/17/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil). RESULTS To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community. CONCLUSIONS Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.
Collapse
Affiliation(s)
- Lukas P Bell-Dereske
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA.
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Laboratory of Environmental Microbiology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská, Prague 4, 1083, 142 20, Czech Republic.
| | - Gian Maria Niccolò Benucci
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Pedro Beschoren da Costa
- Laboratory of Entomology, Department of Plant Sciences, Wageningen University & Research, Wageningen, The Netherlands
| | - Gregory Bonito
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Maren L Friesen
- Department of Plant Pathology, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Lisa K Tiemann
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Sarah E Evans
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
11
|
Fungi associated with woody tissues of Acer pseudoplatanus in forest stands with different health status concerning sooty bark disease (Cryptostroma corticale). Mycol Prog 2023. [DOI: 10.1007/s11557-022-01861-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
AbstractFrom 2018 to 2020, Germany experienced periods of exceptional weather conditions. Extremely high summer temperatures and precipitation deficits induced stress and mortality in forest trees. Acer pseudoplatanus (sycamore) was one of the affected tree species. Symptoms of sooty bark disease (SBD) and severe damage of entire stands, both caused by the fungal species Cryptostroma corticale, were reported more frequently. To explore the non-symptomatic distribution of C. corticale, wood cores from visibly healthy sycamore stems were sampled and all outgrowing fungi were identified and recorded. In total, 50 trees, aged 30–65 years, were sampled at five different forest stands, from which 91 endophytic filamentous morphotypes could be isolated. The fungal endophytic community in the woody tissue of the sycamore trees varied greatly at the different sites and between the trees. The number of isolated morphotypes at the different sites ranged from 13 to 44 and no morphotype was found at all sites. At 1.20-m stem height, 3.3 fungi could be isolated from woody tissue per tree on average. The most abundant species isolated from visibly healthy sycamore in regard to both occurrence at the studied sites and continuity was C. corticale. It was recorded at four of the studied forest stands, from 26% of all studied sycamore trees, and had a frequency of 7.85% relative to the 293 isolated filamentous strains that were isolated. The second most abundant species was Xylaria longipes followed by Lopadostoma turgidum. In this study clear evidence for the endophytic lifestyle of C. corticale is presented which thus appears to be spread further than expected based on visible SBD symptoms.
Collapse
|
12
|
Zhang H, Yang MF, Zhang Q, Yan B, Jiang YL. Screening for broad-spectrum antimicrobial endophytes from Rosa roxburghii and multi-omic analyses of biosynthetic capacity. FRONTIERS IN PLANT SCIENCE 2022; 13:1060478. [PMID: 36466255 PMCID: PMC9709285 DOI: 10.3389/fpls.2022.1060478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Plants with certain medicinal values are a good source for isolating function-specific endophytes. Rosa roxburghii Tratt. has been reported to be a botanical source of antimicrobial compounds, which may represent a promising candidate for screening endophytic fungi with antimicrobial potential. In this study, 54 endophytes were isolated and molecularly identified from R. roxburghii. The preliminary screening using the plate confrontation method resulted in 15 different endophytic strains showing at least one strong inhibition or three or more moderate inhibition against the 12 tested strains. Further re-screening experiments based on the disc diffusion method demonstrated that Epicoccum latusicollum HGUP191049 and Setophoma terrestris HGUP190028 had excellent antagonistic activity. The minimum inhibitory concentration (MIC) test for extracellular metabolites finally indicated that HGUP191049 had lower MIC values and a broader antimicrobial spectrum, compared to HGUP190028. Genomic, non-target metabolomic, and comparative genomic studies were performed to understand the biosynthetic capacity of the screened-out endophytic fungus. Genome sequencing and annotation of HGUP191049 revealed a size of 33.24 megabase pairs (Mbp), with 24 biosynthetic gene clusters (BGCs), where the putative antimicrobial compounds, oxyjavanicin, patulin and squalestatin S1 were encoded by three different BGCs, respectively. In addition, the non-targeted metabolic results demonstrated that the strain contained approximately 120 antimicrobial secondary metabolites and was structurally diverse. Finally, comparative genomics revealed differences in pathogenicity, virulence, and carbohydrate-active enzymes in the genome of Epicoccum spp. Moreover, the results of the comparative analyses presumed that Epicoccum is a promising source of antimicrobial terpenes, while oxyjavanicin and squalestatin S1 are antimicrobial compounds shared by the genus. In conclusion, R. roxburghii and the endophytic HGUP191049 isolated from it are promising sources of broad-spectrum antimicrobial agents.
Collapse
Affiliation(s)
- Hong Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Academy of Testing and Analysis, Guiyang, China
| | - Mao-Fa Yang
- Institute of Entomology, Guizhou University, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Qian Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Bin Yan
- Institute of Entomology, Guizhou University, Guiyang, China
| | - Yu-Lan Jiang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| |
Collapse
|
13
|
Ferreira-Neto JRC, de Araújo FC, de Oliveira Silva RL, de Melo NF, Pandolfi V, Frosi G, de Lima Morais DA, da Silva MD, Rivas R, Santos MG, de Tarso Aidar S, Morgante CV, Benko-Iseppon AM. Dehydration response in Stylosanthes scabra: Transcriptional, biochemical, and physiological modulations. PHYSIOLOGIA PLANTARUM 2022; 174:e13821. [PMID: 36345266 DOI: 10.1111/ppl.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Stylosanthes scabra, popularly known as stylo, is native to the Brazilian Caatinga semiarid region and stands out as a drought-tolerant shrub forage crop. This work provides information about the plant response during the first 48 h of water deficit, followed by a rehydration treatment. Besides root transcriptomics data, 13 physiological or biochemical parameters were scrutinized. Additionally, RNA-Seq annotated transcripts not associated with the "Viridiplantae" clade were taxonomically categorized. It was found that S. scabra quickly perceives and recovers from the oscillations of the imposed water regime. Physiologically, mechanisms that minimize evapotranspiration or protect the photosynthetic apparatus stood out. Biochemically, it was found that the root tissue invests in synthesizing compounds that can act as osmolytes (proline and sugars), emphasizing the importance of osmoregulation to water deficit acclimation. Consistently, transcriptome and qPCR analyses showed that a set of enriched biological processes with upregulated (UR) transcripts were involved in protective functions against reactive oxygen species or encoding enzymes of important metabolic pathways, which might contribute to S. scabra response to water deficit. Additionally, several UR kinases and transcription factors were identified. Finally, in an innovative approach, some naturally occurring microbial groups (such as Schizosaccharomyces, Bradyrhizobium, etc.) were identified in the S. scabra roots. This study reveals insights into the physiological, biochemical, and molecular mechanisms underlying the S. scabra response to water deficit and provides candidate genes that may be useful in developing drought-tolerant crop varieties through biotechnological applications.
Collapse
Affiliation(s)
- José Ribamar Costa Ferreira-Neto
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Flávia Czekalski de Araújo
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Roberta Lane de Oliveira Silva
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | | | - Valesca Pandolfi
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Gabriella Frosi
- Départament de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Manassés Daniel da Silva
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Rebeca Rivas
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Mauro Guida Santos
- Laboratório de Fisiologia Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Saulo de Tarso Aidar
- Empresa Brasileira de Pesquisa Agropecuária (SEMIÁRIDO), Petrolina, Pernambuco, Brazil
| | | | - Ana Maria Benko-Iseppon
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| |
Collapse
|
14
|
Zuo YL, Hu QN, Qin L, Liu JQ, He XL. Species identity and combinations differ in their overall benefits to Astragalus adsurgens plants inoculated with single or multiple endophytic fungi under drought conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:933738. [PMID: 36160950 PMCID: PMC9490189 DOI: 10.3389/fpls.2022.933738] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Although desert plants often establish multiple simultaneous symbiotic associations with various endophytic fungi in their roots, most studies focus on single fungus inoculation. Therefore, combined inoculation of multiple fungi should be applied to simulate natural habitats with the presence of a local microbiome. Here, a pot experiment was conducted to test the synergistic effects between three extremely arid habitat-adapted root endophytes (Alternaria chlamydospora, Sarocladium kiliense, and Monosporascus sp.). For that, we compared the effects of single fungus vs. combined fungi inoculation, on plant morphology and rhizospheric soil microhabitat of desert plant Astragalus adsurgens grown under drought and non-sterile soil conditions. The results indicated that fungal inoculation mainly influenced root biomass of A. adsurgens, but did not affect the shoot biomass. Both single fungus and combined inoculation decreased plant height (7-17%), but increased stem branching numbers (13-34%). However, fungal inoculation influenced the root length and surface area depending on their species and combinations, with the greatest benefits occurring on S. kiliense inoculation alone and its co-inoculation with Monosporascus sp. (109% and 61%; 54% and 42%). Although A. chlamydospora and co-inoculations with S. kiliense and Monosporascus sp. also appeared to promote root growth, these inoculations resulted in obvious soil acidification. Despite no observed root growth promotion, Monosporascus sp. associated with its combined inoculations maximally facilitated soil organic carbon accumulation. However, noticeably, combined inoculation of the three species had no significant effects on root length, surface area, and biomass, but promoted rhizospheric fungal diversity and abundance most, with Sordariomycetes being the dominant fungal group. This indicates the response of plant growth to fungal inoculation may be different from that of the rhizospheric fungal community. Structural equation modeling also demonstrated that fungal inoculation significantly influenced the interactions among the growth of A. adsurgens, soil factors, and rhizospheric fungal groups. Our findings suggest that, based on species-specific and combinatorial effects, endophytic fungi enhanced the plant root growth, altered soil nutrients, and facilitated rhizospheric fungal community, possibly contributing to desert plant performance and ecological adaptability. These results will provide the basis for evaluating the potential application of fungal inoculants for developing sustainable management for desert ecosystems.
Collapse
Affiliation(s)
- Yi-Ling Zuo
- School of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Qian-Nan Hu
- School of Life Sciences, Hebei University, Baoding, China
| | - Le Qin
- School of Life Sciences, Hebei University, Baoding, China
| | - Jia-Qiang Liu
- School of Life Sciences, Hebei University, Baoding, China
| | - Xue-Li He
- School of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| |
Collapse
|
15
|
Chen KH, Liao HL, Arnold AE, Korotkin HB, Wu SH, Matheny PB, Lutzoni F. Comparative transcriptomics of fungal endophytes in co-culture with their moss host Dicranum scoparium reveals fungal trophic lability and moss unchanged to slightly increased growth rates. THE NEW PHYTOLOGIST 2022; 234:1832-1847. [PMID: 35263447 DOI: 10.1111/nph.18078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Mosses harbor fungi whose interactions within their hosts remain largely unexplored. Trophic ranges of fungal endophytes from the moss Dicranum scoparium were hypothesized to encompass saprotrophism. This moss is an ideal host to study fungal trophic lability because of its natural senescence gradient, and because it can be grown axenically. Dicranum scoparium was co-cultured with each of eight endophytic fungi isolated from naturally occurring D. scoparium. Moss growth rates, and gene expression levels (RNA sequencing) of fungi and D. scoparium, were compared between axenic and co-culture treatments. Functional lability of two fungal endophytes was tested by comparing their RNA expression levels when colonizing living vs dead gametophytes. Growth rates of D. scoparium were unchanged, or increased, when in co-culture. One fungal isolate (Hyaloscyphaceae sp.) that promoted moss growth was associated with differential expression of auxin-related genes. When grown with living vs dead gametophytes, Coniochaeta sp. switched from having upregulated carbohydrate transporter activity to upregulated oxidation-based degradation, suggesting an endophytism to saprotrophism transition. However, no such transition was detected for Hyaloscyphaceae sp. Individually, fungal endophytes did not negatively impact growth rates of D. scoparium. Our results support the long-standing hypothesis that some fungal endophytes can switch to saprotrophism.
Collapse
Affiliation(s)
- Ko-Hsuan Chen
- Department of Biology, Duke University, 130 Science Drive, Durham, NC, 27708, USA
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL, 32351, USA
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei, 11529, Taiwan
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL, 32351, USA
- Soil and Water Sciences Department, University of Florida, 1692 McCarty Drive, Gainesville, FL, 32611, USA
| | - A Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, University of Arizona, 1140 E. South Campus Drive, Tucson, AZ, 85721, USA
| | - Hailee B Korotkin
- Department of Ecology and Evolutionary Biology, University of Tennessee, 1416 Circle Drive, Knoxville, TN, 37996, USA
| | - Steven H Wu
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, 1416 Circle Drive, Knoxville, TN, 37996, USA
| | - François Lutzoni
- Department of Biology, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| |
Collapse
|
16
|
Abstract
Alternaria alternata is a common species of fungus frequently isolated from plants as both an endophyte and a pathogen. Although the current definition of A. alternata rests on a foundation of morphological, genetic and genomic analyses, doubts persist regarding the scope of A. alternata within the genus due to the varied symbiotic interactions and wide host range observed in these fungi. These doubts may be due in large part to the history of unstable taxonomy in Alternaria, based on limited morphological characters for species delimitation and host specificity associated with toxins encoded by genes carried on conditionally dispensable chromosomes. This review explores the history of Alternaria taxonomy, focusing in particular on the use of nutritional mode and host associations in species delimitation, with the goal of evaluating A. alternata as it currently stands based on taxonomic best practice. Given the recombination detected among isolates of A. alternata, different symbiotic associations in this species should not be considered phylogenetically informative.
Collapse
Affiliation(s)
- Mara DeMers
- Plant and Microbial Biology Department, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- *Correspondence: Mara DeMers,
| |
Collapse
|
17
|
Fox S, Sikes BA, Brown SP, Cripps CL, Glassman SI, Hughes K, Semenova-Nelsen T, Jumpponen A. Fire as a driver of fungal diversity - A synthesis of current knowledge. Mycologia 2022; 114:215-241. [PMID: 35344467 DOI: 10.1080/00275514.2021.2024422] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Fires occur in most terrestrial ecosystems where they drive changes in the traits, composition, and diversity of fungal communities. Fires range from rare, stand-replacing wildfires to frequent, prescribed fires used to mimic natural fire regimes. Fire regime factors, including burn severity, fire intensity, and timing, vary widely and likely determine how fungi respond to fires. Despite the importance of fungi to post-fire plant communities and ecosystem functioning, attempts to identify common fungal responses and their major drivers are lacking. This synthesis addresses this knowledge gap and ranges from fire adaptations of specific fungi to succession and assembly fungal communities as they respond to spatially heterogenous burning within the landscape. Fires impact fungi directly and indirectly through their effects on fungal survival, substrate and habitat modifications, changes in environmental conditions, and/or physiological responses of the hosts with which fungi interact. Some specific pyrophilous, or "fire-loving," fungi often appear after fire. Our synthesis explores whether such taxa can be considered cosmopolitan, and whether they are truly fire-adapted or simply opportunists adapted to rapidly occupy substrates and habitats made available by fires. We also discuss the possible inoculum sources of post-fire fungi and explore existing conceptual models and ecological frameworks that may be useful in generalizing fungal fire responses. We conclude with identifying research gaps and areas that may best transform the current knowledge and understanding of fungal responses to fire.
Collapse
Affiliation(s)
- Sam Fox
- Division of Biology, Kansas State University, Manhattan, Kansas 66506.,Department of Natural Resources and Society, University of Idaho, Moscow, Idaho 83844
| | - Benjamin A Sikes
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045
| | - Shawn P Brown
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152
| | - Cathy L Cripps
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717
| | - Sydney I Glassman
- Department of Microbiology & Plant Pathology, University of California at Riverside, Riverside, California 92521
| | - Karen Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee at Knoxville, Knoxville, Tennessee 37996
| | - Tatiana Semenova-Nelsen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| |
Collapse
|
18
|
Das P, Effmert U, Baermann G, Quella M, Piechulla B. Impact of bacterial volatiles on phytopathogenic fungi: an in vitro study on microbial competition and interaction. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:596-614. [PMID: 34718549 DOI: 10.1093/jxb/erab476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms in the rhizosphere are abundant and exist in very high taxonomic diversity. The major players are bacteria and fungi, and bacteria have evolved many strategies to prevail over fungi, among them harmful enzyme activities and noxious secondary metabolites. Interactions between plant growth promoting rhizobacteria and phytopathogenic fungi are potentially valuable since the plant would benefit from fungal growth repression. In this respect, the role of volatile bacterial metabolites in fungistasis has been demonstrated, but the mechanisms of action are less understood. We used three phytopathogenic fungal species (Sclerotinia sclerotiorum, Rhizoctonia solani, and Juxtiphoma eupyrena) as well as one non-phytopathogenic species (Neurospora crassa) and the plant growth promoting rhizobacterium Serratia plymuthica 4Rx13 in co-cultivation assays to investigate the influence of bacterial volatile metabolites on fungi on a cellular level. As a response to the treatment, we found elevated lipid peroxidation, which indirectly reflected the loss of fungal cell membrane integrity. An increase in superoxide dismutase, catalase, and laccase activities indicated oxidative stress. Acclimation to these adverse growth conditions completely restored fungal growth. One of the bioactive bacterial volatile compounds seemed to be ammonia, which was a component of the bacterial volatile mixture. Applied as a single compound in biogenic concentrations ammonia also caused an increase in lipid peroxidation and enzyme activities, but the extent and pattern did not fully match the effect of the entire bacterial volatile mixture.
Collapse
Affiliation(s)
- Piyali Das
- Institute of Biological Sciences, Biochemistry, Albert-Einstein-Strasse 3, University of Rostock, 18059 Rostock, Germany
| | - Uta Effmert
- Institute of Biological Sciences, Biochemistry, Albert-Einstein-Strasse 3, University of Rostock, 18059 Rostock, Germany
| | - Gunnar Baermann
- Institute of Biological Sciences, Biochemistry, Albert-Einstein-Strasse 3, University of Rostock, 18059 Rostock, Germany
| | - Manuel Quella
- Institute of Biological Sciences, Biochemistry, Albert-Einstein-Strasse 3, University of Rostock, 18059 Rostock, Germany
| | - Birgit Piechulla
- Institute of Biological Sciences, Biochemistry, Albert-Einstein-Strasse 3, University of Rostock, 18059 Rostock, Germany
| |
Collapse
|
19
|
Itagaki H, Hosoya T. Lifecycle of Pyrenopeziza protrusa ( Helotiales, Dermateaceae sensu lato) in Magnolia obovata revealed by field observation and molecular quantification. MYCOSCIENCE 2021; 62:373-381. [PMID: 37090175 PMCID: PMC9721505 DOI: 10.47371/mycosci.2021.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
Fungi exhibit saprophytic, parasitic, and symbiotic lifestyles, and flexibly switching between them by the environmental changes and host conditions. However, only a few studies have elucidated the detailed changes in fungal DNA or morphology, including the formation of reproductive structures along with lifestyle switching. We hypothesized that Pyrenopeziza protrusa, which occurs abundantly and specifically on Magnolia obovata as a saprophyte, is also associated with living hosts and switches its lifestyles as part of its lifecycle. To elucidate this hypothesis, we periodically sampled the fresh/fallen leaves of M. obovata to observe the seasonal occurrence of reproductive structures for the isolation and detection/quantification of P. protrusa DNA with newly developed species-specific primers. The isolation frequency and amount of P. protrusa DNA drastically increased in the fresh leaves just before defoliation in autumn, but remained high in fallen leaves from autumn to spring. Abundant production of conidiomata and apothecia was also observed in the fallen leaves with increasing DNA content. These results clarified a large part of the lifecycle of P. protrusa, suggesting that the lifestyle is switched from symbiotic to saprophytic stage by significantly increasing the amount of DNA in response to host conditions according to the seasonal variations.
Collapse
Affiliation(s)
- Hiyori Itagaki
- Department of Biological Science, Graduate School of Science, The University of Tokyo
| | | |
Collapse
|
20
|
Gómez OC, Moreira DMB, Luiz JHH. Medicinal potentialities and pathogenic profile of Lasiodiplodia genus. World J Microbiol Biotechnol 2021; 37:190. [PMID: 34632549 DOI: 10.1007/s11274-021-03137-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022]
Abstract
Considering that current biotechnological advances have been contributing towards improving the well-being of humanity, endophytic fungi, such as Lasiodiplodia, are promising sources of new substances to be used in chemical, pharmaceutical and agrochemical processes. Bioactive secondary metabolites are examples of such substances, although it is widely known that Lasiodiplodia inflicts irreparable damage to several crops of major economic importance. They are often produced as a response against biotic and abiotic factors, thus revealing that they play different roles, such as in signaling and defense mechanisms. Therefore, this review presents a few subtle differences between pathogenicity and mutualistic endophyte-host interactions. Moreover, the main secondary metabolites produced by Lasiodiplodia endophytes have been described with respect to their relevant antimicrobial and cytotoxic activities.
Collapse
Affiliation(s)
- Omar Cabezas Gómez
- Chemistry Institute, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil
| | | | | |
Collapse
|
21
|
An automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant pathogens. Sci Rep 2021; 11:19731. [PMID: 34611252 PMCID: PMC8492765 DOI: 10.1038/s41598-021-99363-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/16/2021] [Indexed: 01/29/2023] Open
Abstract
Fungal plant-pathogens promote infection of their hosts through the release of 'effectors'-a broad class of cytotoxic or virulence-promoting molecules. Effectors may be recognised by resistance or sensitivity receptors in the host, which can determine disease outcomes. Accurate prediction of effectors remains a major challenge in plant pathology, but if achieved will facilitate rapid improvements to host disease resistance. This study presents a novel tool and pipeline for the ranking of predicted effector candidates-Predector-which interfaces with multiple software tools and methods, aggregates disparate features that are relevant to fungal effector proteins, and applies a pairwise learning to rank approach. Predector outperformed a typical combination of secretion and effector prediction methods in terms of ranking performance when applied to a curated set of confirmed effectors derived from multiple species. We present Predector ( https://github.com/ccdmb/predector ) as a useful tool for the ranking of predicted effector candidates, which also aggregates and reports additional supporting information relevant to effector and secretome prediction in a simple, efficient, and reproducible manner.
Collapse
|
22
|
Hopke A, Mela A, Ellett F, Carter-House D, Peña JF, Stajich JE, Altamirano S, Lovett B, Egan M, Kale S, Kronholm I, Guerette P, Szewczyk E, McCluskey K, Breslauer D, Shah H, Coad BR, Momany M, Irimia D. Crowdsourced analysis of fungal growth and branching on microfluidic platforms. PLoS One 2021; 16:e0257823. [PMID: 34587206 PMCID: PMC8480888 DOI: 10.1371/journal.pone.0257823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/10/2021] [Indexed: 01/16/2023] Open
Abstract
Fungal hyphal growth and branching are essential traits that allow fungi to spread and proliferate in many environments. This sustained growth is essential for a myriad of applications in health, agriculture, and industry. However, comparisons between different fungi are difficult in the absence of standardized metrics. Here, we used a microfluidic device featuring four different maze patterns to compare the growth velocity and branching frequency of fourteen filamentous fungi. These measurements result from the collective work of several labs in the form of a competition named the "Fungus Olympics." The competing fungi included five ascomycete species (ten strains total), two basidiomycete species, and two zygomycete species. We found that growth velocity within a straight channel varied from 1 to 4 μm/min. We also found that the time to complete mazes when fungal hyphae branched or turned at various angles did not correlate with linear growth velocity. We discovered that fungi in our study used one of two distinct strategies to traverse mazes: high-frequency branching in which all possible paths were explored, and low-frequency branching in which only one or two paths were explored. While the high-frequency branching helped fungi escape mazes with sharp turns faster, the low-frequency turning had a significant advantage in mazes with shallower turns. Future work will more systematically examine these trends.
Collapse
Affiliation(s)
- Alex Hopke
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Shriners Hospital for Children, Boston, Massachusetts, United States of America
| | - Alex Mela
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, Georgia, United States of America
| | - Felix Ellett
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Derreck Carter-House
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Jesús F. Peña
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Sophie Altamirano
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brian Lovett
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| | - Martin Egan
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Shiv Kale
- Nutritional Immunology and Molecular Medicine Institute, Blacksburg, Virginia, United States of America
| | - Ilkka Kronholm
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Paul Guerette
- Bolt Threads Inc., Emeryville, California, United States of America
| | - Edyta Szewczyk
- Bolt Threads Inc., Emeryville, California, United States of America
| | - Kevin McCluskey
- Bolt Threads Inc., Emeryville, California, United States of America
| | - David Breslauer
- Bolt Threads Inc., Emeryville, California, United States of America
| | - Hiral Shah
- Bharat Chattoo Genome Research Centre, Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Bryan R. Coad
- School of Agriculture, Food & Wine, University of Adelaide, Adelaide, South Australia, Australia
| | - Michelle Momany
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, Georgia, United States of America
- * E-mail: (DI); (MM)
| | - Daniel Irimia
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Shriners Hospital for Children, Boston, Massachusetts, United States of America
- * E-mail: (DI); (MM)
| |
Collapse
|
23
|
Jones DAB, Moolhuijzen PM, Hane JK. Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi. Microb Genom 2021; 7. [PMID: 34468307 PMCID: PMC8715435 DOI: 10.1099/mgen.0.000637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Plant diseases caused by fungal pathogens are typically initiated by molecular interactions between 'effector' molecules released by a pathogen and receptor molecules on or within the plant host cell. In many cases these effector-receptor interactions directly determine host resistance or susceptibility. The search for fungal effector proteins is a developing area in fungal-plant pathology, with more than 165 distinct confirmed fungal effector proteins in the public domain. For a small number of these, novel effectors can be rapidly discovered across multiple fungal species through the identification of known effector homologues. However, many have no detectable homology by standard sequence-based search methods. This study employs a novel comparison method (RemEff) that is capable of identifying protein families with greater sensitivity than traditional homology-inference methods, leveraging a growing pool of confirmed fungal effector data to enable the prediction of novel fungal effector candidates by protein family association. Resources relating to the RemEff method and data used in this study are available from https://figshare.com/projects/Effector_protein_remote_homology/87965.
Collapse
Affiliation(s)
- Darcy A B Jones
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia
| | - Paula M Moolhuijzen
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia
| | - James K Hane
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia.,Curtin Institute for Computation, Curtin University, Perth, Australia
| |
Collapse
|
24
|
Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes. Int J Mol Sci 2021; 22:ijms22136791. [PMID: 34202675 PMCID: PMC8268838 DOI: 10.3390/ijms22136791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.
Collapse
|
25
|
de Vries S, de Vries J, Archibald JM, Slamovits CH. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. FEMS Microbiol Ecol 2021; 96:5904760. [PMID: 32918444 PMCID: PMC7585586 DOI: 10.1093/femsec/fiaa184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022] Open
Abstract
Oomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them with (i) 22 oomycete genomes and (ii) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify a S. sapeloensis-specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. Salisapilia sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.
Collapse
Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada.,Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany.,Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany.,Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany.,Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| |
Collapse
|
26
|
Papp LA, Ács-Szabó L, Póliska S, Miklós I. A modified culture medium and hyphae isolation method can increase quality of the RNA extracted from mycelia of a dimorphic fungal species. Curr Genet 2021; 67:823-830. [PMID: 33837814 PMCID: PMC8405466 DOI: 10.1007/s00294-021-01181-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/20/2021] [Accepted: 03/23/2021] [Indexed: 11/22/2022]
Abstract
The capability of RNA isolation with good efficiency and high quality is essential for a downstream application such as RNA sequencing. It requires successful cell culturing and an effective RNA isolation method. Although effective methods are available, production of the homogenous mycelia and extraction of good-quality mycelial RNA from true invasive hyphae, which penetrated into the agar plates, are difficult. To overcome these problems, the aim of this study was to develop technical modifications which allow production of homogenous mycelial biomass without extra stimuli agents and improve quality of the RNA extracted from the fungal hyphae. Our alternative culture medium was suitable for production both yeast-phase cells and hyphae of the Schizosaccharomyces japonicus and other dimorphic species, such as the Candida albicans, Saccharomyces cerevisiae, and Jaminaea angkorensis. To improve quality of the mycelial RNA, we developed an isolation procedure of the hyphal tip, which eliminated the unnecessary vacuoles-containing parts of the hyphae. To increase RNA quantity, we used glass beads in the RNA extraction protocol to achieve stronger breaking of the mycelial walls. All these modifications can also be useful for researchers working with other dimorphic fungi and can contribute to the higher comparability of the transcriptional data coming from yeast-phase cells and hyphae or even from different species.
Collapse
Affiliation(s)
- László Attila Papp
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Lajos Ács-Szabó
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Szilárd Póliska
- Department of Biochemistry and Molecular Biology, Faculty of General Medicine, University of Debrecen, Debrecen, Hungary
| | - Ida Miklós
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| |
Collapse
|
27
|
Putative LysM Effectors Contribute to Fungal Lifestyle. Int J Mol Sci 2021; 22:ijms22063147. [PMID: 33808705 PMCID: PMC8003418 DOI: 10.3390/ijms22063147] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 11/17/2022] Open
Abstract
Fungal LysM effector proteins can dampen plant host–defence responses, protecting hyphae from plant chitinases, but little is known on these effectors from nonpathogenic fungal endophytes. We found four putative LysM effectors in the genome of the endophytic nematophagous fungus Pochonia chlamydosporia (Pc123). All four genes encoding putative LysM effectors are expressed constitutively by the fungus. Additionally, the gene encoding Lys1—the smallest one—is the most expressed in banana roots colonised by the fungus. Pc123 Lys1, 2 and 4 display high homology with those of other strains of the fungus and phylogenetically close entomopathogenic fungi. However, Pc123 Lys3 displays low homology with other fungi, but some similarities are found in saprophytes. This suggests evolutionary divergence in Pc123 LysM effectors. Additionally, molecular docking shows that the NAcGl binding sites of Pc123 Lys 2, 3 and 4 are adjacent to an alpha helix. Putative LysM effectors from fungal endophytes, such as Pc123, differ from those of plant pathogenic fungi. LysM motifs from endophytic fungi show clear conservation of cysteines in Positions 13, 51 and 63, unlike those of plant pathogens. LysM effectors could therefore be associated with the lifestyle of a fungus and give us a clue of how organisms could behave in different environments.
Collapse
|
28
|
Gladieux P, De Bellis F, Hann-Soden C, Svedberg J, Johannesson H, Taylor JW. Neurospora from Natural Populations: Population Genomics Insights into the Life History of a Model Microbial Eukaryote. Methods Mol Biol 2021; 2090:313-336. [PMID: 31975173 DOI: 10.1007/978-1-0716-0199-0_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiated by Stanford geneticist David Perkins, the genus Neurospora has also become a basic model for the study of evolutionary processes, speciation, and population biology. In this chapter, we will first trace the history that brought Neurospora into the era of population genomics. We will then cover the major contributions of population genomic investigations using Neurospora to our understanding of microbial biogeography and speciation, and review recent work using population genomics and genome-wide association mapping that illustrates the unique potential of Neurospora as a model for identifying the genetic basis of (potentially adaptive) phenotypes in filamentous fungi. The advent of population genomics has contributed to firmly establish Neurospora as a complete model system and we hope our review will entice biologists to include Neurospora in their research.
Collapse
Affiliation(s)
- Pierre Gladieux
- UMR BGPI, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | - Fabien De Bellis
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Christopher Hann-Soden
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jesper Svedberg
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| |
Collapse
|
29
|
Protection of surplus food from fungal spoilage using Streptomyces spp.: a green approach. Arch Microbiol 2020; 203:941-950. [PMID: 33089339 DOI: 10.1007/s00203-020-02087-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 10/06/2020] [Indexed: 02/04/2023]
Abstract
Consortia of Streptomyces spp. (colonies 169, 194, 165 and 130) used in this study are an efficient producer of secondary metabolites like chitinases and antifungal compounds, which may help in the protection of surplus food from spoilage. Qualitative screening for chitinase production and taxonomy of these colonies were undertaken in our previous studies. In the current study, GC-MS analysis of extract produced from the consortia of Streptomyces strains was done for the identification of antifungal compounds. Treatment of surplus food with activated consortia of Streptomyces spp. has protected powdered food for a month, whereas fresh food (unpowdered) was preserved for two days. A control sample of surplus food (untreated) was kept to check the contamination, which resulted in the growth of three fungi (FP-1, FG-1, and FB-1). Taxonomic characterization of fungi and identification of toxic compounds produced from them were done by ITS amplification and GC-MS analysis, respectively. The study shows that the secondary metabolites from Streptomyces spp. have the potential to protect the food from mycotoxin contamination. Based on literature reports, this is for the first time that bioactive compounds and chitinases produced from Streptomyces are being used for the protection and management of surplus food.
Collapse
|
30
|
Endophytes: Colonization, Behaviour, and Their Role in Defense Mechanism. Int J Microbiol 2020; 2020:6927219. [PMID: 32802073 PMCID: PMC7414354 DOI: 10.1155/2020/6927219] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/28/2020] [Accepted: 07/01/2020] [Indexed: 11/18/2022] Open
Abstract
Biotic and abiotic factors cause an enormous amount of yield and economical loss. However, endophytes can play a significant role in enhancing the tolerance of plants. Endophytes systematically colonize different parts of the host, but plants use a variety of defense mechanisms towards microbial infection. However, they have to survive the oxidative environments, and endophytes like Enterobacter sp. encode superoxide dismutases, catalases, and hydroperoxide reductases to cope up the oxidative stress during colonization. On the contrary, others produce subtilomycin which binds with flagella to affect flg22-induced plant defense. The behavior of endophytes can be affected by different genes in hydrolase activity when they come into contact with the host plant. The lifestyle of endophytes is influenced by environmental factors, the host, and microbial genotypes, as well as an imbalance in nutrient exchange between the microbe and the host. For instance, induction of PiAMT1 in root endophyte Piriformospora indica indicates depletion of nitrogen which plays as a triggering factor for activation of the saprotrophic program. Microbes enhance disease resistance through induced systemic resistance (ISR), and Bacillus cereus triggers ISR against Botrytis cinerea through an accumulation of the PR1 protein and activates MAPK signaling and WRKY53 gene expression by the JA/ET signaling pathway. Similarly, Trichoderma arundinaceum produces trichodiene that affects Botrytis cinerea through induction of defense-related genes encoding salicylic acid (SA) and jasmonate (JA). Overall, endophytes can play a vital role in disease management.
Collapse
|
31
|
Guhr A, Kircher S. Drought-Induced Stress Priming in Two Distinct Filamentous Saprotrophic Fungi. MICROBIAL ECOLOGY 2020; 80:27-33. [PMID: 31950228 PMCID: PMC7338827 DOI: 10.1007/s00248-019-01481-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/22/2019] [Indexed: 05/04/2023]
Abstract
Sessile organisms constantly face environmental fluctuations and especially drought is a common stressor. One adaptive mechanism is "stress priming," the ability to cope with a severe stress ("triggering") by retaining information from a previous mild stress event ("priming"). While plants have been extensively investigated for drought-induced stress priming, no information is available for saprotrophic filamentous fungi, which are highly important for nutrient cycles. Here, we investigated the potential for drought-induced stress priming of one strain each of two ubiquitous species, Neurospora crassa and Penicillium chrysogenum. A batch experiment with 4 treatments was conducted on a sandy soil: exposure to priming and/or triggering as well as non-stressed controls. A priming stress was caused by desiccation to pF 4. The samples were then rewetted and after 1-, 7-, or 14-days of recovery triggered (pF 6). After triggering, fungal biomass, respiration, and β-glucosidase activity were quantified. P. chrysogenum showed positive stress priming effects. After 1 day of recovery, biomass as well as β-glucosidase activity and respiration were 0.5 to 5 times higher during triggering. Effects on biomass and activity decreased with prolonged recovery but lasted for 7 days and minor effects were still detectable after 14 days. Without triggering, stress priming had a temporary negative impact on biomass but this reversed after 14 days. For N. crassa, no stress priming effect was observed on the tested variables. The potential for drought-induced stress priming seems to be species specific with potentially high impact on composition and activity of fungal communities considering the expected increase of drought events.
Collapse
Affiliation(s)
- Alexander Guhr
- Department of Soil Ecology, BayCEER, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95448, Bayreuth, Germany.
| | - Sophia Kircher
- Department of Soil Ecology, BayCEER, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95448, Bayreuth, Germany
| |
Collapse
|
32
|
Prunus trees in Germany—a hideout of unknown fungi? Mycol Prog 2020. [DOI: 10.1007/s11557-020-01586-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractPrunus belongs to the economically most important genera of fruit crops in Germany. Although wood pathogens possess the capability to damage the host substantially, the knowledge of the fungal pathogenic community and the mycobiome of Prunus wood in general is low. During a survey in important fruit production areas in Germany, branches with symptoms of fungal infection were sampled in Prunus avium, P. cerasus and P. domestica orchards, and 1018 fungal isolates were obtained primarily from the transition zone of symptomatic to non-symptomatic wood. By a combination of blastn searches and phylogenetic analyses based on ITS and LSU sequences with a strong focus on reliable reference data, a diversity of 172 fungal taxa belonging to Ascomycota, Basidiomycota and Mucoromycota were differentiated. The majority of the strains belonged to three classes of Ascomycota, namely Sordariomycetes, Leotiomycetes and Dothideomycetes. The dominant species were Aposphaeria corallinolutea (Dothideomycetes) and Pallidophorina paarla (Leotiomycetes) that were isolated more than a hundred times each, while all other taxa were isolated ≤ 30 times. Only part of them could be identified to species level. Because of the high plasticity of species boundaries, the identification certainty was divided into categories based on nucleotide differences to reference sequences. In total, 82 species were identified with high and 20 species with low (cf.) certainty. Moreover, about 70 species could not be assigned to a known species, which reveals Prunus wood to represent a habitat harbouring high numbers of potentially new species, even in a well-explored region like Germany.
Collapse
|
33
|
Herzog S, Brinkmann H, Vences M, Fleißner A. Evidence of repeated horizontal transfer of sterol C-5 desaturase encoding genes among dikarya fungi. Mol Phylogenet Evol 2020; 150:106850. [PMID: 32438044 DOI: 10.1016/j.ympev.2020.106850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 01/26/2023]
Abstract
Gene duplication and horizontal gene transfer (HGT) are two important but different forces for adaptive genome evolution. In eukaryotic organisms, gene duplication is considered to play a more important evolutionary role than HGT. However, certain fungal lineages have developed highly efficient mechanisms that avoid the occurrence of duplicated gene sequences within their genomes. While these mechanisms likely originated as a defense against harmful mobile genetic elements, they come with an evolutionary cost. A prominent example for a genome defense system is the RIP mechanism of the ascomycete fungus Neurospora crassa, which efficiently prevents sequence duplication within the genome and functional redundancy of the subsequent paralogs. Despite this tight control, the fungus possesses two functionally redundant sterol C-5 desaturase enzymes, ERG-10a and ERG-10b, that catalyze the same step during ergosterol biosynthesis. In this study, we addressed this conundrum by phylogenetic analysis of the two proteins and supporting topology tests. We obtained evidence that a primary HGT of a sterol C-5 desaturase gene from Tremellales (an order of Basidiomycota) into a representative of the Pezizomycotina (a subphylum of Ascomycota) is the origin of the ERG-10b sequence. The reconstructed phylogenies suggest that this HGT event was followed by multiple HGT events among other members of the Pezizomycotina, thereby generating a diverse group with members in the four classes Sordariomycetes, Xylonomycetes, Eurotiomycetes and Dothideomycetes, which all harbor the second sterol C-5 desaturase or maintained in some cases only the ERG-10b version of this enzyme. These results furnish an example for a gene present in numerous ascomycetous fungi but primarily acquired by an ancestral HGT event from another fungal phylum. Furthermore, these data indicate that HGT represents one mechanism to generate functional redundancy in organisms with a strict avoidance of gene duplications.
Collapse
Affiliation(s)
- Stephanie Herzog
- Institut für Genetik, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Henner Brinkmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Miguel Vences
- Zoologisches Institut, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - André Fleißner
- Institut für Genetik, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany.
| |
Collapse
|
34
|
Sternhagen EC, Black KL, Hartmann EDL, Shivega WG, Johnson PG, McGlynn RD, Schmaltz LC, Asheim Keller RJ, Vink SN, Aldrich-Wolfe L. Contrasting Patterns of Functional Diversity in Coffee Root Fungal Communities Associated with Organic and Conventionally Managed Fields. Appl Environ Microbiol 2020; 86:e00052-20. [PMID: 32220838 PMCID: PMC7237791 DOI: 10.1128/aem.00052-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/16/2020] [Indexed: 11/20/2022] Open
Abstract
The structure and function of fungal communities in the coffee rhizosphere are influenced by crop environment. Because coffee can be grown along a management continuum from conventional application of pesticides and fertilizers in full sun to organic management in a shaded understory, we used coffee fields to hold host constant while comparing rhizosphere fungal communities under markedly different environmental conditions with regard to shade and inputs. We characterized the shade and soil environment in 25 fields under conventional, organic, or transitional management in two regions of Costa Rica. We amplified the internal transcribed spacer 2 (ITS2) region of fungal DNA from coffee roots in these fields and characterized the rhizosphere fungal community via high-throughput sequencing. Sequences were assigned to guilds to determine differences in functional diversity and trophic structure among coffee field environments. Organic fields had more shade, a greater richness of shade tree species, and more leaf litter and were less acidic, with lower soil nitrate availability and higher soil copper, calcium, and magnesium availability than conventionally managed fields, although differences between organic and conventionally managed fields in shade and calcium and magnesium availability depended on region. Differences in richness and community composition of rhizosphere fungi between organic and conventionally managed fields were also correlated with shade, soil acidity, and nitrate and copper availability. Trophic structure differed with coffee field management. Saprotrophs, plant pathogens, and mycoparasites were more diverse, and plant pathogens were more abundant, in organic than in conventionally managed fields, while saprotroph-plant pathogens were more abundant in conventionally managed fields. These differences reflected environmental differences and depended on region.IMPORTANCE Rhizosphere fungi play key roles in ecosystems as nutrient cyclers, pathogens, and mutualists, yet little is currently known about which environmental factors and how agricultural management may influence rhizosphere fungal communities and their functional diversity. This field study of the coffee agroecosystem suggests that organic management not only fosters a greater overall diversity of fungi, but it also maintains a greater richness of saprotrophic, plant-pathogenic, and mycoparasitic fungi that has implications for the efficiency of nutrient cycling and regulation of plant pathogen populations in agricultural systems. As well as influencing community composition and richness of rhizosphere fungi, shade management and use of fungicides and synthetic fertilizers altered the trophic structure of the coffee agroecosystem.
Collapse
Affiliation(s)
- Elizabeth C Sternhagen
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Katie L Black
- Biology Department, Concordia College, Moorhead, Minnesota, USA
| | | | - W Gaya Shivega
- Biology Department, Concordia College, Moorhead, Minnesota, USA
| | - Peter G Johnson
- Biology Department, Concordia College, Moorhead, Minnesota, USA
| | - Riley D McGlynn
- Biology Department, Concordia College, Moorhead, Minnesota, USA
| | | | | | - Stefanie N Vink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Laura Aldrich-Wolfe
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| |
Collapse
|
35
|
Carreón-Anguiano KG, Islas-Flores I, Vega-Arreguín J, Sáenz-Carbonell L, Canto-Canché B. EffHunter: A Tool for Prediction of Effector Protein Candidates in Fungal Proteomic Databases. Biomolecules 2020; 10:biom10050712. [PMID: 32375409 PMCID: PMC7277995 DOI: 10.3390/biom10050712] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/17/2020] [Accepted: 03/21/2020] [Indexed: 11/16/2022] Open
Abstract
Pathogens are able to deliver small-secreted, cysteine-rich proteins into plant cells to enable infection. The computational prediction of effector proteins remains one of the most challenging areas in the study of plant fungi interactions. At present, there are several bioinformatic programs that can help in the identification of these proteins; however, in most cases, these programs are managed independently. Here, we present EffHunter, an easy and fast bioinformatics tool for the identification of effectors. This predictor was used to identify putative effectors in 88 proteomes using characteristics such as size, cysteine residue content, secretion signal and transmembrane domains.
Collapse
Affiliation(s)
- Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Julio Vega-Arreguín
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores-UNAM, León, México
| | - Luis Sáenz-Carbonell
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| |
Collapse
|
36
|
Hane JK, Paxman J, Jones DAB, Oliver RP, de Wit P. "CATAStrophy," a Genome-Informed Trophic Classification of Filamentous Plant Pathogens - How Many Different Types of Filamentous Plant Pathogens Are There? Front Microbiol 2020; 10:3088. [PMID: 32038539 PMCID: PMC6986263 DOI: 10.3389/fmicb.2019.03088] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022] Open
Abstract
The traditional classification of fungal and oomycete phytopathogens into three classes – biotrophs, hemibiotrophs, or necrotrophs – is unsustainable. This study highlights multiple phytopathogen species for which these labels have been inappropriately applied. We propose a novel and reproducible classification based solely on genome-derived analysis of carbohydrate-active enzyme (CAZyme) gene content called CAZyme-Assisted Training And Sorting of -trophy (CATAStrophy). CATAStrophy defines four major divisions for species associated with living plants. These are monomertrophs (Mo) (corresponding to biotrophs), polymertrophs (P) (corresponding to necrotrophs), mesotrophs (Me) (corresponding to hemibiotrophs), and vasculartrophs (including species commonly described as wilts, rots, or anthracnoses). The Mo class encompasses symbiont, haustorial, and non-haustorial species. Me are divided into the subclasses intracellular and extracellular Me, and the P into broad and narrow host sub-classes. This gives a total of seven discrete plant-pathogenic classes. The classification provides insight into the properties of these species and offers a facile route to develop control measures for newly recognized diseases. Software for CATAStrophy is available online at https://github.com/ccdmb/catastrophy. We present the CATAStrophy method for the prediction of trophic phenotypes based on CAZyme gene content, as a complementary method to the traditional tripartite “biotroph–hemibiotroph–necrotroph” classifications that may encourage renewed investigation and revision within the fungal biology community.
Collapse
Affiliation(s)
- James K Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.,Curtin Institute for Computation, Faculty of Science and Engineering, Curtin University, Perth, WA, Australia
| | - Jonathan Paxman
- Department of Mechanical Engineering, Curtin University, Perth, WA, Australia
| | - Darcy A B Jones
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Pierre de Wit
- Laboratory of Phytopathology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| |
Collapse
|
37
|
Martins MP, Martinez-Rossi NM, Sanches PR, Gomes EV, Bertolini MC, Pedersoli WR, Silva RN, Rossi A. The pH Signaling Transcription Factor PAC-3 Regulates Metabolic and Developmental Processes in Pathogenic Fungi. Front Microbiol 2019; 10:2076. [PMID: 31551996 PMCID: PMC6738131 DOI: 10.3389/fmicb.2019.02076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/22/2019] [Indexed: 01/22/2023] Open
Abstract
The zinc finger transcription factor PAC-3/RIM101/PacC has a defined role in the secretion of enzymes and proteins in response to ambient pH, and also contributes to the virulence of species. Herein we evaluated the role of PAC-3 in the regulation of Neurospora crassa genes, in a model that examined the plant-fungi interactions. N. crassa is a model fungal species capable of exhibiting dynamic responses to its environment by employing endophytic or phytopathogenic behavior according to a given circumstance. Since plant growth and productivity are highly affected by pH and phosphorus (P) acquisition, we sought to verify the impact that induction of a Δpac-3 mutation would have under limited and sufficient Pi availability, while ensuring that the targeted physiological adjustments mimicked ambient pH and nutritional conditions required for efficient fungal growth and development. Our results suggest direct regulatory functions for PAC-3 in cell wall biosynthesis, homeostasis, oxidation-reduction processes, hydrolase activity, transmembrane transport, and modulation of genes associated with fungal virulence. Pi-dependent modulation was observed mainly in genes encoding for transporter proteins or related to cell wall development, thereby advancing the current understanding regarding colonization and adaptation processes in response to challenging environments. We have also provided comprehensive evidence that suggests a role for PAC-3 as a global regulator in plant pathogenic fungi, thus presenting results that have the potential to be applied to various types of microbes, with diverse survival mechanisms.
Collapse
Affiliation(s)
- Maíra Pompeu Martins
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Nilce M Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Pablo R Sanches
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Maria Célia Bertolini
- Department of Biochemistry and Technological Chemistry, São Paulo State University, UNESP, Institute of Chemistry, Araraquara, Brazil
| | - Wellington R Pedersoli
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Antonio Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| |
Collapse
|
38
|
Zhao Z, Ying Y, Hung YS, Tang Y. Genome Mining Reveals Neurospora crassa Can Produce the Salicylaldehyde Sordarial. JOURNAL OF NATURAL PRODUCTS 2019; 82:1029-1033. [PMID: 30908040 PMCID: PMC6933945 DOI: 10.1021/acs.jnatprod.8b00983] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A highly reducing polyketide synthase gene cluster from the Magnaporthe oryzae genome was previously identified to produce phytotoxic compounds including pyriculol. A homologous gene cluster was found in Neurospora crassa through bioinformatics analysis. Heterologous expression of this cluster led to the production of the salicylic aldehyde sordarial and related intermediates. A series of combinatorial gene expression experiments established the set of enzymes required to produce sordarial and the likely biosynthetic pathway.
Collapse
Affiliation(s)
- Zhiyue Zhao
- Department of Chemical and Biomolecular Engineering
| | - Youmin Ying
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Yiu-Sun Hung
- Department of Chemical and Biomolecular Engineering
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, U. S. A
| |
Collapse
|
39
|
Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa. mBio 2019; 10:mBio.00192-19. [PMID: 30914504 PMCID: PMC6437048 DOI: 10.1128/mbio.00192-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Fungal spores germinate and undergo vegetative growth, leading to either asexual or sexual reproductive dispersal. Previous research has indicated that among developmental regulatory genes, expression is conserved across nutritional environments, whereas pathways for carbon and nitrogen metabolism appear highly responsive-perhaps to accommodate differential nutritive processing. To comprehensively investigate conidial germination and the adaptive life history decision-making underlying these two modes of reproduction, we profiled transcription of Neurospora crassa germinating on two media: synthetic Bird medium, designed to promote asexual reproduction; and a natural maple sap medium, on which both asexual reproduction and sexual reproduction manifest. A later start to germination but faster development was observed on synthetic medium. Metabolic genes exhibited altered expression in response to nutrients-at least 34% of the genes in the genome were significantly downregulated during the first two stages of conidial germination on synthetic medium. Knockouts of genes exhibiting differential expression across development altered germination and growth rates, as well as in one case causing abnormal germination. A consensus Bayesian network of these genes indicated especially tight integration of environmental sensing, asexual and sexual development, and nitrogen metabolism on a natural medium, suggesting that in natural environments, a more dynamic and tentative balance of asexual and sexual development may be typical of N. crassa colonies.IMPORTANCE One of the most remarkable successes of life is its ability to flourish in response to temporally and spatially varying environments. Fungi occupy diverse ecosystems, and their sensitivity to these environmental changes often drives major fungal life history decisions, including the major switch from vegetative growth to asexual or sexual reproduction. Spore germination comprises the first and simplest stage of vegetative growth. We examined the dependence of this early life history on the nutritional environment using genome-wide transcriptomics. We demonstrated that for developmental regulatory genes, expression was generally conserved across nutritional environments, whereas metabolic gene expression was highly labile. The level of activation of developmental genes did depend on current nutrient conditions, as did the modularity of metabolic and developmental response network interactions. This knowledge is critical to the development of future technologies that could manipulate fungal growth for medical, agricultural, or industrial purposes.
Collapse
|
40
|
Forest Tree Microbiomes and Associated Fungal Endophytes: Functional Roles and Impact on Forest Health. FORESTS 2019. [DOI: 10.3390/f10010042] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Terrestrial plants including forest trees are generally known to live in close association with microbial organisms. The inherent features of this close association can be commensalism, parasitism or mutualism. The term “microbiota” has been used to describe this ecological community of plant-associated pathogenic, mutualistic, endophytic and commensal microorganisms. Many of these microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Comparatively, studies on forest tree microbiomes and their roles in mutualism and disease lag far behind parallel work on crop and human microbiome projects. Very recently, our understanding of plant and tree microbiomes has been enriched due to novel technological advances using metabarcoding, metagenomics, metatranscriptomics and metaproteomics approaches. In addition, the availability of massive DNA databases (e.g., NCBI (USA), EMBL (Europe), DDBJ (Japan), UNITE (Estonia)) as well as powerful computational and bioinformatics tools has helped to facilitate data mining by researchers across diverse disciplines. Available data demonstrate that plant phyllosphere bacterial communities are dominated by members of only a few phyla (Proteobacteria, Actinobacteria, Bacteroidetes). In bulk forest soil, the dominant fungal group is Basidiomycota, whereas Ascomycota is the most prevalent group within plant tissues. The current challenge, however, is how to harness and link the acquired knowledge on microbiomes for translational forest management. Among tree-associated microorganisms, endophytic fungal biota are attracting a lot of attention for their beneficial health- and growth-promoting effects, and were preferentially discussed in this review.
Collapse
|
41
|
Zeng Z, Wu J, Kovalchuk A, Raffaello T, Wen Z, Liu M, Asiegbu FO. Genome-wide DNA methylation and transcriptomic profiles in the lifestyle strategies and asexual development of the forest fungal pathogen Heterobasidion parviporum. Epigenetics 2019; 14:16-40. [PMID: 30633603 PMCID: PMC6380393 DOI: 10.1080/15592294.2018.1564426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/03/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022] Open
Abstract
Heterobasidion parviporum is the most devastating fungal pathogen of conifer forests in Northern Europe. The fungus has dual life strategies, necrotrophy on living trees and saprotrophy on dead woods. DNA cytosine methylation is an important epigenetic modification in eukaryotic organisms. Our presumption is that the lifestyle transition and asexual development in H. parviporum could be driven by epigenetic effects. Involvements of DNA methylation in the regulation of aforementioned processes have never been studied thus far. RNA-seq identified lists of highly induced genes enriched in carbohydrate-active enzymes during necrotrophic interaction with host trees and saprotrophic sawdust growth. It also highlighted signaling- and transcription factor-related genes potentially associated with the transition of saprotrophic to necrotrophic lifestyle and groups of primary cellular activities throughout asexual development. Whole-genome bisulfite sequencing revealed that DNA methylation displayed pronounced preference in CpG dinucleotide context across the genome and mostly targeted transposable element (TE)-rich regions. TE methylation level demonstrated a strong negative correlation with TE expression, reinforcing the protective function of DNA methylation in fungal genome stability. Small groups of genes putatively subject to methylation transcriptional regulation in response to saprotrophic and necrotrophic growth in comparison with free-living mycelia were also explored. Our study reported on the first methylome map of a forest pathogen. Analysis of transcriptome and methylome variations associated with asexual development and different lifestyle strategies provided further understanding of basic biological processes in H. parviporum. More importantly, our work raised additional potential roles of DNA methylation in fungi apart from controlling the proliferation of TEs.
Collapse
Affiliation(s)
- Zhen Zeng
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Jiayao Wu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Tommaso Raffaello
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Zilan Wen
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Mengxia Liu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Fred O. Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
42
|
|
43
|
Chen KH, Liao HL, Arnold AE, Bonito G, Lutzoni F. RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi. THE NEW PHYTOLOGIST 2018; 218:1597-1611. [PMID: 29604236 DOI: 10.1111/nph.15092] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/07/2018] [Indexed: 05/15/2023]
Abstract
Diverse plant-associated fungi are thought to have symbiotrophic and saprotrophic states because they can be isolated from both dead and living plant tissues. However, such tissues often are separated in time and space, and fungal activity at various stages of plant senescence is rarely assessed directly in fungal community studies. We used fungal ribosomal RNA metatranscriptomics to detect active fungal communities across a natural senescence gradient within wild-collected gametophytes of Dicranum scoparium (Bryophyta) to understand the distribution of active fungal communities in adjacent living, senescing and dead tissues. Ascomycota were active in all tissues across the senescence gradient. By contrast, Basidiomycota were prevalent and active in senescing and dead tissues. Several fungi were detected as active in living and dead tissues, suggesting their capacity for multi-trophy. Differences in community assembly detected by metatranscriptomics were echoed by amplicon sequencing of cDNA and compared to culture-based inferences and observation of fungal fruit bodies in the field. The combination of amplicon sequencing of cDNA and metatranscriptomics is promising for studying symbiotic systems with complex microbial diversity, allowing for the simultaneous detection of their presence and activity.
Collapse
Affiliation(s)
- Ko-Hsuan Chen
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Hui-Ling Liao
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Soil and Water Sciences Department, North Florida Research and Education Center, University of Florida, Quincy, FL, 32351, USA
| | - A Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | |
Collapse
|
44
|
Casarrubia S, Daghino S, Kohler A, Morin E, Khouja HR, Daguerre Y, Veneault-Fourrey C, Martin FM, Perotto S, Martino E. The Hydrophobin-Like OmSSP1 May Be an Effector in the Ericoid Mycorrhizal Symbiosis. FRONTIERS IN PLANT SCIENCE 2018; 9:546. [PMID: 29765384 PMCID: PMC5938622 DOI: 10.3389/fpls.2018.00546] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
Mutualistic and pathogenic plant-colonizing fungi use effector molecules to manipulate the host cell metabolism to allow plant tissue invasion. Some small secreted proteins (SSPs) have been identified as fungal effectors in both ectomycorrhizal and arbuscular mycorrhizal fungi, but it is currently unknown whether SSPs also play a role as effectors in other mycorrhizal associations. Ericoid mycorrhiza is a specific endomycorrhizal type that involves symbiotic fungi mostly belonging to the Leotiomycetes (Ascomycetes) and plants in the family Ericaceae. Genomic and RNASeq data from the ericoid mycorrhizal fungus Oidiodendron maius led to the identification of several symbiosis-upregulated genes encoding putative SSPs. OmSSP1, the most highly symbiosis up-regulated SSP, was found to share some features with fungal hydrophobins, even though it lacks the Pfam hydrophobin domain. Sequence alignment with other hydrophobins and hydrophobin-like fungal proteins placed OmSSP1 within Class I hydrophobins. However, the predicted features of OmSSP1 may suggest a distinct type of hydrophobin-like proteins. The presence of a predicted signal peptide and a yeast-based signal sequence trap assay demonstrate that OmSSP1 is secreted. OmSSP1 null-mutants showed a reduced capacity to form ericoid mycorrhiza with Vaccinium myrtillus roots, suggesting a role as effectors in the ericoid mycorrhizal interaction.
Collapse
Affiliation(s)
- Salvatore Casarrubia
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Stefania Daghino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Annegret Kohler
- INRA (Institut National de la Recherche Agronomique), UMR 1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, Champenoux, France
| | - Emmanuelle Morin
- INRA (Institut National de la Recherche Agronomique), UMR 1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, Champenoux, France
| | | | - Yohann Daguerre
- INRA (Institut National de la Recherche Agronomique), UMR 1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, Champenoux, France
| | - Claire Veneault-Fourrey
- INRA (Institut National de la Recherche Agronomique), UMR 1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, Champenoux, France
- Université de Lorraine, UMR 1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Faculté des Sciences et Technologies, Vandoeuvre les Nancy, France
| | - Francis M. Martin
- INRA (Institut National de la Recherche Agronomique), UMR 1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, Champenoux, France
| | - Silvia Perotto
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Elena Martino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- INRA (Institut National de la Recherche Agronomique), UMR 1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, Champenoux, France
| |
Collapse
|
45
|
|
46
|
Adam A, Deimel S, Pardo-Medina J, García-Martínez J, Konte T, Limón MC, Avalos J, Terpitz U. Protein Activity of the Fusarium fujikuroi Rhodopsins CarO and OpsA and Their Relation to Fungus-Plant Interaction. Int J Mol Sci 2018; 19:ijms19010215. [PMID: 29324661 PMCID: PMC5796164 DOI: 10.3390/ijms19010215] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/23/2017] [Accepted: 01/08/2018] [Indexed: 01/25/2023] Open
Abstract
Fungi possess diverse photosensory proteins that allow them to perceive different light wavelengths and to adapt to changing light conditions in their environment. The biological and physiological roles of the green light-sensing rhodopsins in fungi are not yet resolved. The rice plant pathogen Fusarium fujikuroi exhibits two different rhodopsins, CarO and OpsA. CarO was previously characterized as a light-driven proton pump. We further analyzed the pumping behavior of CarO by patch-clamp experiments. Our data show that CarO pumping activity is strongly augmented in the presence of the plant hormone indole-3-acetic acid and in sodium acetate, in a dose-dependent manner under slightly acidic conditions. By contrast, under these and other tested conditions, the Neurospora rhodopsin (NR)-like rhodopsin OpsA did not exhibit any pump activity. Basic local alignment search tool (BLAST) searches in the genomes of ascomycetes revealed the occurrence of rhodopsin-encoding genes mainly in phyto-associated or phytopathogenic fungi, suggesting a possible correlation of the presence of rhodopsins with fungal ecology. In accordance, rice plants infected with a CarO-deficient F. fujikuroi strain showed more severe bakanae symptoms than the reference strain, indicating a potential role of the CarO rhodopsin in the regulation of plant infection by this fungus.
Collapse
Affiliation(s)
- Alexander Adam
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, D-97074 Würzburg, Germany; (A.A.); (S.D.)
| | - Stephan Deimel
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, D-97074 Würzburg, Germany; (A.A.); (S.D.)
| | - Javier Pardo-Medina
- Department of Genetics, Faculty of Biology, University of Seville, E-41012 Seville, Spain; (J.P.-M.); (J.G.-M.); (M.C.L.); (J.A.)
| | - Jorge García-Martínez
- Department of Genetics, Faculty of Biology, University of Seville, E-41012 Seville, Spain; (J.P.-M.); (J.G.-M.); (M.C.L.); (J.A.)
| | - Tilen Konte
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Sl-1000 Ljubljana, Slovenia;
| | - M. Carmen Limón
- Department of Genetics, Faculty of Biology, University of Seville, E-41012 Seville, Spain; (J.P.-M.); (J.G.-M.); (M.C.L.); (J.A.)
| | - Javier Avalos
- Department of Genetics, Faculty of Biology, University of Seville, E-41012 Seville, Spain; (J.P.-M.); (J.G.-M.); (M.C.L.); (J.A.)
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, D-97074 Würzburg, Germany; (A.A.); (S.D.)
- Correspondence: ; Tel.: +49-931-31-84226
| |
Collapse
|
47
|
Zhou J, Li X, Huang PW, Dai CC. Endophytism or saprophytism: Decoding the lifestyle transition of the generalist fungus Phomopsis liquidambari. Microbiol Res 2018; 206:99-112. [DOI: 10.1016/j.micres.2017.10.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/28/2017] [Accepted: 10/10/2017] [Indexed: 01/09/2023]
|
48
|
Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLoS Genet 2017; 13:e1006867. [PMID: 28704372 PMCID: PMC5509106 DOI: 10.1371/journal.pgen.1006867] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/13/2017] [Indexed: 12/29/2022] Open
Abstract
Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.
Collapse
Affiliation(s)
- Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America
| | - Zheng Wang
- Department of Biostatistics, Yale University, New Haven, CT, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Kayla Stefanko
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Caitlyn Cubba
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale University, New Haven, CT, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States of America
| |
Collapse
|
49
|
McCluskey K, Baker SE. Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era. Mycology 2017; 8:67-83. [PMID: 30123633 PMCID: PMC6059044 DOI: 10.1080/21501203.2017.1281849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 01/14/2023] Open
Abstract
Filamentous fungi have been important as model organisms since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycete filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Similarly, shared data has contributed to the success of model systems. The scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.
Collapse
Affiliation(s)
- Kevin McCluskey
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Scott E. Baker
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| |
Collapse
|
50
|
Baral B. Entomopathogenicity and Biological Attributes of Himalayan Treasured Fungus Ophiocordyceps sinensis (Yarsagumba). J Fungi (Basel) 2017; 3:E4. [PMID: 29371523 PMCID: PMC5715966 DOI: 10.3390/jof3010004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/20/2017] [Accepted: 01/31/2017] [Indexed: 01/01/2023] Open
Abstract
Members of the entomophagous fungi are considered very crucial in the fungal domain relative to their natural phenomenon and economic perspectives; however, inadequate knowledge of their mechanisms of interaction keeps them lagging behind in parallel studies of fungi associated with agro-ecology, forest pathology and medical biology. Ophiocordyceps sinensis (syn. Cordyceps sinensis), an intricate fungus-caterpillar complex after it parasitizes the larva of the moth, is a highly prized medicinal fungus known widely for ages due to its peculiar biochemical assets. Recent technological innovations have significantly contributed a great deal to profiling the variable clinical importance of this fungus and other related fungi with similar medicinal potential. However, a detailed mechanism behind fungal pathogenicity and fungal-insect interactions seems rather ambiguous and is poorly justified, demanding special attention. The goal of the present review is to divulge an update on the published data and provides promising insights on different biological events that have remained underemphasized in previous reviews on fungal biology with relation to life-history trade-offs, host specialization and selection pressures. The infection of larvae by a fungus is not a unique event in Cordyceps; hence, other fungal species are also reviewed for effective comparison. Conceivably, the rationale and approaches behind the inheritance of pharmacological abilities acquired and stored within the insect framework at a time when they are completely hijacked and consumed by fungal parasites, and the molecular mechanisms involved therein, are clearly documented.
Collapse
Affiliation(s)
- Bikash Baral
- Research, Community Development and Conservation Center (C3DR), Pokhara 33700, Nepal.
- Department of Biochemistry, University of Turku, Turku, Finn-20014, Finland.
| |
Collapse
|