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Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RDC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol 2024; 9:336-345. [PMID: 38316926 PMCID: PMC10847041 DOI: 10.1038/s41564-023-01575-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/29/2023] [Indexed: 02/07/2024]
Abstract
microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.
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Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paulo Wender P Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Andres M Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Emily C Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, Norman, OK, USA
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, San Diego, CA, USA
| | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Sara L Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, Johannesburg, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ian A Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula C Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Santos, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Matthew F Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Daniel Alvarado-Villalobos
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, MD, USA
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Nyon, Switzerland
| | | | - Berenike C Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Daniel Petras
- Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department for Metabolomics, Kiel University, Kiel, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- King's College London, London, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
| | | | - Alicia Isabel Pérez-Lorente
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Carlos Molina-Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Diego Romero
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | | | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jerry J Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Hector H F Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Sidnee E Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, Eugene, OR, USA
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
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Scott K, Konkel Z, Gluck-Thaler E, Valero David GE, Simmt CF, Grootmyers D, Chaverri P, Slot J. Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma. PLoS One 2023; 18:e0289280. [PMID: 38127903 PMCID: PMC10735191 DOI: 10.1371/journal.pone.0289280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/14/2023] [Indexed: 12/23/2023] Open
Abstract
Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichoderma's diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.
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Affiliation(s)
- Kelsey Scott
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Emile Gluck-Thaler
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
| | | | - Coralie Farinas Simmt
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
| | - Django Grootmyers
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Priscila Chaverri
- Department of Natural Sciences, Bowie State University, Bowie, MD, United States of America
- School of Biology and Natural Products Research Center (CIPRONA), University of Costa Rica, San José, Costa Rica
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
- Center for Psychedelic Drug Research and Education, The Ohio State University, Columbus, OH, United States of America
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Chaverri P, Romberg MK, Montero-Vargas M, McKemy JM, Rane KK, Balbalian CJ, Castlebury LA. Phylogeographic and Phylogenomic Structure of the Quarantine Plant Pathogen Colletotrichum liriopes, Including New Reports in the United States. Plant Dis 2023; 107:2816-2824. [PMID: 36802295 DOI: 10.1094/pdis-10-22-2324-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Global agricultural trade has accelerated the emergence and re-emergence of new plant pathogens. In the United States, the fungal pathogen Colletotrichum liriopes is still considered a foreign quarantine pathogen that affects ornamental plants (i.e., Liriope spp.). Even though this species has been reported in East Asia on various asparagaceous hosts, its first and only report in the United States was in 2018. However, that study used only ITS nrDNA for identification, and no available culture or voucher specimen was maintained. The main objective of the present study was to determine the geographic and host distribution of specimens identified as C. liriopes. To accomplish this, new and existing isolates, sequences, and genomes obtained from various hosts and geographic locations (i.e., China, Colombia, Mexico, and the United States) were compared with the ex-type of C. liriopes. Multilocus phylogenetic (ITS, Tub2, GAPDH, CHS-1, and HIS3), phylogenomic, and splits tree analyses revealed that all the studied isolates/sequences form a well-supported clade with little intraspecific variation. Morphological characterizations support these findings. The minimum spanning network, low nucleotide diversity, and negative Tajima's D from both multilocus and genomic data suggest that there was a recent movement/invasion of a few East Asian genotypes to other countries where the ornamental plants are produced (e.g., South America) and subsequently to the importing countries, such as the United States. The study reveals that the geographic and host distribution of C. liriopes sensu stricto is expanded to the United States (i.e., at least Maryland, Mississippi, and Tennessee) and on various hosts in addition to Asparagaceae and Orchidaceae. The present study produces fundamental knowledge that can be used in efforts to reduce costs or losses from agricultural trade and to expand our understanding of pathogen movement.
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Affiliation(s)
- Priscila Chaverri
- USDA ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705, U.S.A
- Oak Ridge Institute for Science and Education, USDA ARS Research Participation Program, Oak Ridge, TN 37830, U.S.A
- Department of Natural Sciences, Bowie State University, Bowie, MD 20715, U.S.A
| | | | - Maripaz Montero-Vargas
- Advanced Computing Laboratory, Costa Rica National High Technology Center (CeNAT), San José, Costa Rica
| | | | - Karen K Rane
- Plant Diagnostic Laboratory, University of Maryland, College Park, MD 20742, U.S.A
| | - Clarissa J Balbalian
- Plant Diagnostic Laboratory, Mississippi State University, Mississippi State, MS 39762, U.S.A
| | - Lisa A Castlebury
- USDA ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705, U.S.A
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Escudero-Leyva E, Quirós-Guerrero L, Vásquez-Chaves V, Pereira-Reyes R, Chaverri P, Tamayo-Castillo G. Differential Volatile Organic Compound Expression in the Interaction of Daldinia eschscholtzii and Mycena citricolor. ACS Omega 2023; 8:31373-31388. [PMID: 37663497 PMCID: PMC10468842 DOI: 10.1021/acsomega.3c03865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023]
Abstract
Fungi exhibit a wide range of ecological guilds, but those that live within the inner tissues of plants (also known as endophytes) are particularly relevant due to the benefits they sometimes provide to their hosts, such as herbivory deterrence, disease protection, and growth promotion. Recently, endophytes have gained interest as potential biocontrol agents against crop pathogens, for example, coffee plants (Coffea arabica). Published results from research performed in our laboratory showed that endophytic fungi isolated from wild Rubiaceae plants were effective in reducing the effects of the American leaf spot of coffee (Mycena citricolor). One of these isolates (GU11N) from the plant Randia grandifolia was identified as Daldinia eschscholtzii (Xylariales). Its antagonism mechanisms, effects, and chemistry against M. citricolor were investigated by analyzing its volatile profile alone and in the presence of the pathogen in contactless and dual culture assays. The experimental design involved direct sampling of agar plugs in vials for headspace (HS) and headspace solid-phase microextraction (HS-SPME) gas chromatography-mass spectrometry (GC-MS) analysis. Additionally, we used ultrahigh-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS/MS) to identify nonvolatile compounds from organic extracts of the mycelia involved in the interaction. Results showed that more volatile compounds were identified using HS-SPME (39 components) than those by the HS technique (13 components), sharing only 12 compounds. Statistical tests suggest that D. eschscholtzii inhibited the growth of M. citricolor through the release of VOCs containing a combination of 1,8-dimethoxynapththalene and terpene compounds affecting M. citricolor pseudopilei. The damaging effects of 1,8-dimethoxynaphthalene were corroborated in an in vitro test against M. citricolor pseudopilei; scanning electron microscopy (SEM) photographs confirmed structural damage. After analyzing the UHPLC-HRMS/MS data, a predominance of fatty acid derivatives was found among the putatively identified compounds. However, a considerable proportion of features (37.3%) remained unannotated. In conclusion, our study suggests that D. eschscholtzii has potential as a biocontrol agent against M. citricolor and that 1,8-dimethoxynaphthalene contributes to the observed damage to the pathogen's reproductive structures.
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Affiliation(s)
- Efraín Escudero-Leyva
- Centro
de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11520-2060 San José, Costa Rica
- Escuela
de Biología, Universidad de Costa
Rica, 11520-2060 San José, Costa Rica
| | - Luis Quirós-Guerrero
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1205 Geneva, Switzerland
- School
of Pharmaceutical Sciences, University of
Geneva, 1205 Geneva, Switzerland
| | - Víctor Vásquez-Chaves
- Centro
de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11520-2060 San José, Costa Rica
| | - Reinaldo Pereira-Reyes
- Laboratorio
Nacional de Nanotecnología (LANOTEC), Centro Nacional de Alta Tecnología, 10109 San Jose, Costa Rica
| | - Priscila Chaverri
- Centro
de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11520-2060 San José, Costa Rica
- Escuela
de Biología, Universidad de Costa
Rica, 11520-2060 San José, Costa Rica
- Department
of Natural Sciences, Bowie State University, Bowie, Maryland 20715, United States
| | - Giselle Tamayo-Castillo
- Centro
de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11520-2060 San José, Costa Rica
- Escuela
de Química, Universidad de Costa
Rica, 11520-2060 San José, Costa Rica
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5
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Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SLL, Barbera GL, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O’Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. Res Sq 2023:rs.3.rs-3189768. [PMID: 37577622 PMCID: PMC10418563 DOI: 10.21203/rs.3.rs-3189768/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health.
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Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Paulo Wender P. Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Andres M. Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Allegra T. Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, United States
| | - Emily C. Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Michael J. Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Nicole E. Avalon
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, United States
| | - Robert H. Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Mirte C. M. Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Sara L. Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, 178 Montecasino Boulevard, Fourways, Johannesburg, Gauteng, 2191, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Private Bag X5050, Thohoyandou, Limpopo, 950, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Paula C. Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Rua Carvalho de Mendonça, 144, Santos, SP, 11070-100, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 319 Life Sciences Building, University Park, PA, 16802, United States
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 320 Life Sciences Building, University Park, PA, 16802, United States
| | - Matthew F. Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States
| | - Daniel Alvarado-Villalobos
- Metabolomics & Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics & Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) & Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, 20715, United States
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Department of Biology, University of Fribourg, Chemin du Musée, 10, Fribourg, FR, 1700, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - William H. Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland
| | - Josep Massana-Codina
- Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland
| | - Berenike C. Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany
| | - Daniel Petras
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Auf der Morgenstelle 24, Tuebingen, 72076, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, United States
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women’s University, Cheongpa-ro 47 gil 100, Seoul, 04310, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- King’s College London, Strand, London, WC2R 2LS, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 110 Scripps Way, Jupiter, FL, 33458, United States
| | - Mariana Silva dos Santos
- Metabolomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alicia Isabel Pérez-Lorente
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Carlos Molina-Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Diego Romero
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, 38124, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark
| | - Martin Frederik Laursen
- National Food Institute, Technical University of Denmark, Kemitorvet B202, Lyngby, 2800, Denmark
| | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Technikerstr. 25, Innsbruck, 6020, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14,, Vienna, 1090, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02142, United States
| | - Ellis Charles O’Neill
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Xueli Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, Singapore, 636921, Singapore
| | - Jerry J. Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Center for Applied Plant Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Infectious Diseases Institute, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Av. Costa e Silva, s/n, Campo Grande, MS, 79070-900, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Av. Costa e Silva, s/n, Campo Grande, MS, 79070-900, Brazil
| | | | - Hector H. F. Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, 1777 Carvalho Leal Avenue, Manaus, AM, 69065-001, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Jason A. Clement
- Baruch S. Blumberg Institute, 3805 Old Easton Rd., Doylestown, PA, 18902, United States
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, United States
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL, 61604, United States
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Weniger Hall, room 341, Corvallis, OR, 97331, United States
| | - Sidnee E. Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, 1255 E 13th Ave, Basement, Eugene, OR, 97402, United States
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, 900 University Ave., Riverside, CA, 92521, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
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6
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Escudero-Leyva E, Del Milagro Granados-Montero M, Orozco-Ortiz C, Araya-Valverde E, Alvarado-Picado E, Chaves-Fallas JM, Aldrich-Wolfe L, Chaverri P. The endophytobiome of wild Rubiaceae as a source of antagonistic fungi against the American Leaf Spot of coffee (Mycena citricolor). J Appl Microbiol 2023; 134:7146202. [PMID: 37113015 DOI: 10.1093/jambio/lxad090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/26/2023] [Indexed: 04/29/2023]
Abstract
AIMS The American leaf spot, caused by Mycena citricolor, is an important disease of coffee (Coffea arabica), mostly in Central America. Currently, there are limited pathogen control alternatives that are environmentally friendly and economically accessible. The use of fungi isolated from the plant endomycobiota in their native habitats is on the rise because studies show their great potential for biological control. To begin to generate a green alternative to control M. citricolor, the objectives of the present study were to (i) collect, identify, screen (in vitro and in planta), and select endophytic fungi from wild Rubiaceae collected in old-growth forests of Costa Rica; (ii) confirm endophytic colonization in coffee plantlets; (iii) evaluate the effects of the endophytes on plantlet development; and (iv) corroborate the antagonistic ability in planta. METHODS AND RESULTS Through in vitro and in planta antagonism assays, we found that out of the selected isolates (i.e., Daldinia eschscholzii GU11N, Nectria pseudotrichia GUHN1, Purpureocillium aff. lilacinum CT24, Sarocladium aff. kiliense CT25, Trichoderma rifaii CT5, T. aff. crassum G1C, T. aff. atroviride G7T, T. aff. strigosellum GU12, and Xylaria multiplex GU14T), Trichoderma spp. produced the highest growth inhibition percentages in vitro. Trichoderma isolates CT5 and G1C were then tested in planta using Coffea arabica cv. caturra plantlets. Endophytic colonization was verified, followed by in planta growth promotion and antagonism assays. CONCLUSIONS Results show that Trichoderma isolates CT5 and G1C have potential for plant growth promotion and antagonism against Mycena citricolor, reducing incidence and severity, and preventing plant mortality.
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Affiliation(s)
- Efraín Escudero-Leyva
- Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, Pavas, San José, Costa Rica
| | - María Del Milagro Granados-Montero
- Escuela de Agronomía, Estación Experimental Fabio Baudrit and Centro de Investigaciones en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Cristofer Orozco-Ortiz
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, Pavas, San José, Costa Rica
| | - Emmanuel Araya-Valverde
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, Pavas, San José, Costa Rica
| | - Eduardo Alvarado-Picado
- Centro para el Desarrollo de Alternativas Orgánicas (CeDAO), San Marcos de Tarrazú, San José, Costa Rica
| | - José Miguel Chaves-Fallas
- Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Laura Aldrich-Wolfe
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Priscila Chaverri
- Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, USA
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7
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Rojas-Gätjens D, Avey-Arroyo J, Chaverri P, Rojas-Jimenez K, Chavarría M. Differences in fungal communities in the fur of two- and three-toed sloths revealed by ITS metabarcoding. Microbiology (Reading) 2023; 169. [PMID: 36848210 DOI: 10.1099/mic.0.001309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Sloths have dense fur on which insects, algae, bacteria and fungi coexist. Previous studies using cultivation-dependent methods and 18S rRNA sequencing revealed that the fungal communities in their furs comprise members of the phyla Ascomycota and Basidiomycota. In this note, we increase the resolution and knowledge of the mycobiome inhabiting the fur of the two- (Choloepus hoffmanni) and three-toed (Bradypus variegatus) sloths. Targeted amplicon metagenomic analysis of ITS2 nrDNA sequences obtained from 10 individuals of each species inhabiting the same site revealed significant differences in the structure of their fungal communities and also in the alpha-diversity estimators. The results suggest a specialization by host species and that the host effect is stronger than that of sex, age and animal weight. Capnodiales were the dominant order in sloths' fur and Cladosporium and Neodevriesia were the most abundant genera in Bradypus and Choloepus, respectively. The fungal communities suggest that the green algae that inhabit the fur of sloths possibly live lichenized with Ascomycota fungal species. The data shown in this note offer a more detailed view of the fungal content in the fur of these extraordinary animals and could help explain other mutualistic relationships in this complex ecosystem.
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Affiliation(s)
- Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | | | - Priscila Chaverri
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Keilor Rojas-Jimenez
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
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8
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Castro-Moretti FR, Cocuron JC, Castillo-Gonzalez H, Escudero-Leyva E, Chaverri P, Guerreiro-Filho O, Slot JC, Alonso AP. A metabolomic platform to identify and quantify polyphenols in coffee and related species using liquid chromatography mass spectrometry. Front Plant Sci 2023; 13:1057645. [PMID: 36684722 PMCID: PMC9852862 DOI: 10.3389/fpls.2022.1057645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Products of plant secondary metabolism, such as phenolic compounds, flavonoids, alkaloids, and hormones, play an important role in plant growth, development, stress resistance. The plant family Rubiaceae is extremely diverse and abundant in Central America and contains several economically important genera, e.g. Coffea and other medicinal plants. These are known for the production of bioactive polyphenols (e.g. caffeine and quinine), which have had major impacts on human society. The overall goal of this study was to develop a high-throughput workflow to identify and quantify plant polyphenols. METHODS First, a method was optimized to extract over 40 families of phytochemicals. Then, a high-throughput metabolomic platform has been developed to identify and quantify 184 polyphenols in 15 min. RESULTS The current metabolomics study of secondary metabolites was conducted on leaves from one commercial coffee variety and two wild species that also belong to the Rubiaceae family. Global profiling was performed using liquid chromatography high-resolution time-of-flight mass spectrometry. Features whose abundance was significantly different between coffee species were discriminated using statistical analysis and annotated using spectral databases. The identified features were validated by commercially available standards using our newly developed liquid chromatography tandem mass spectrometry method. DISCUSSION Caffeine, trigonelline and theobromine were highly abundant in coffee leaves, as expected. Interestingly, wild Rubiaceae leaves had a higher diversity of phytochemicals in comparison to commercial coffee: defense-related molecules, such as phenylpropanoids (e.g., cinnamic acid), the terpenoid gibberellic acid, and the monolignol sinapaldehyde were found more abundantly in wild Rubiaceae leaves.
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Affiliation(s)
- Fernanda R. Castro-Moretti
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | | | - Humberto Castillo-Gonzalez
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Efrain Escudero-Leyva
- School of Biology and Natural Products Research Center Centro de Investigaciones en Productos Naturales (CIPRONA), University of Costa Rica, San Jose, Costa Rica
- Centro Nacional de Alta Technologia-Consejo Nacional de Rectores (CeNAT-CONARE), National Center for Biotechnological Innovations (CENIBiot), San Jose, Costa Rica
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
- School of Biology and Natural Products Research Center Centro de Investigaciones en Productos Naturales (CIPRONA), University of Costa Rica, San Jose, Costa Rica
| | | | - Jason C. Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States
| | - Ana Paula Alonso
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
- BioAnalytical Facility, University of North Texas, Denton, TX, United States
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9
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Escudero-Leyva E, Vieto S, Avendaño R, Rojas-Gätjens D, Agüero P, Pacheco C, Montero ML, Chaverri P, Chavarría M. Fungi with history: Unveiling the mycobiota of historic documents of Costa Rica. PLoS One 2023; 18:e0279914. [PMID: 36652424 PMCID: PMC9847896 DOI: 10.1371/journal.pone.0279914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/18/2022] [Indexed: 01/19/2023] Open
Abstract
We studied the physicochemical characteristics and mycobiota associated to five key historic documents from Costa Rica, including the Independence Act of Costa Rica from 1821. We used nondestructive techniques (i.e., ATR-FTIR and XRF) to determine paper and ink composition. Results show that some documents are composed of cotton-based paper, whereas others were made of wood cellulose with an increased lignin content. We also determined that the ink employed in some of the documents is ferrogallic. Cultivation and molecular techniques were used to characterize the fungi inhabiting the documents. In total, 22 fungal isolates were obtained: 15 from the wood-cellulose-based documents and seven from the other three cotton-based. We also tested the cellulolytic activity of the recovered fungi; 95% of the fungi presented cellulolytic activity correlated to their ability to cause deterioration of the paper. Results suggest that cotton-based paper is the most resistant to fungal colonization and that most of the isolates have cellulolytic activity. This work increases the knowledge of the fungal diversity that inhabits historic documents and its relationship with paper composition and provides valuable information to develop strategies to conserve and restore these invaluable documents.
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Affiliation(s)
- Efraín Escudero-Leyva
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Sofía Vieto
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Paola Agüero
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | | | - Mavis L. Montero
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Ciencia e Ingeniería de Materiales (CICIMA), Universidad de Costa Rica, San José, Costa Rica
| | - Priscila Chaverri
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, United States of America
- * E-mail: (PC); (MC)
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
- * E-mail: (PC); (MC)
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10
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Campos-Esquivel L, Hanson PE, Escudero-Leyva E, Chaverri P. Virulence of native isolates of entomopathogenic fungi (Hypocreales) against the "sweetpotato whitefly" Bemisia tabaci (Hemiptera: Aleyrodidae), including the effects of temperature and fungicides. J Invertebr Pathol 2022; 192:107787. [PMID: 35697117 DOI: 10.1016/j.jip.2022.107787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/04/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
Hypocrella, Moelleriella and related species in the Hypocreales (Ascomycota, Sordariomycetes) cause epizootics of whiteflies and scale insects in nature. However, studies on their host specificity, virulence, infection cycles, optimal development under laboratory conditions, and compatibility with other control methods, are unexplored for most species. Under laboratory conditions, the virulence of several isolates of field-collected hypocrealean fungi (Hypocrella, Moelleriella, Regiocrella, and Verticillium) was determined on Bemisia tabaci eggs and 4th instar nymphs. In addition to virulence, the effect of temperature and two commercial fungicides on growth rates and germination of the isolates was evaluated. None of the isolates infected the eggs, while M. libera, M. ochracea, and M. turbinata caused high nymphal mortality. Moelleriella libera was the most virulent isolate. At all temperatures, M. libera, Regiocrella sp. (P17H20), and Verticillium cf. pseudohemipterigenum had the highest germination and growth rates. The optimal growth temperature depended on the isolate, but at 23 °C and 25 °C, the probability of spore germination was higher for most isolates. Finally, the fungicides azoxystrobin and chlorothalonil inhibited growth rates and conidial germination at 24 and 48 h of exposure. This research produces vital knowledge on the virulence and infection cycles of poorly studied native species of entomopathogenic fungi. In addition, the results provide information on the optimal temperature for development in laboratory conditions and susceptibility to fungicides, which could contribute to future biological control strategies.
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Affiliation(s)
| | - Paul E Hanson
- Escuela de Biología, Universidad de Costa Rica, 11501-2060 San José, Costa Rica
| | - Efraín Escudero-Leyva
- Escuela de Biología, Universidad de Costa Rica, 11501-2060 San José, Costa Rica; Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
| | - Priscila Chaverri
- Escuela de Biología, Universidad de Costa Rica, 11501-2060 San José, Costa Rica; Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060 San José, Costa Rica.
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11
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Crous PW, Sandoval-Denis M, Costa MM, Groenewald JZ, van Iperen AL, Starink-Willemse M, Hernández-Restrepo M, Kandemir H, Ulaszewski B, de Boer W, Abdel-Azeem AM, Abdollahzadeh J, Akulov A, Bakhshi M, Bezerra JDP, Bhunjun CS, Câmara MPS, Chaverri P, Vieira WAS, Decock CA, Gaya E, Gené J, Guarro J, Gramaje D, Grube M, Gupta VK, Guarnaccia V, Hill R, Hirooka Y, Hyde KD, Jayawardena RS, Jeewon R, Jurjević Ž, Korsten L, Lamprecht SC, Lombard L, Maharachchikumbura SSN, Polizzi G, Rajeshkumar KC, Salgado-Salazar C, Shang QJ, Shivas RG, Summerbell RC, Sun GY, Swart WJ, Tan YP, Vizzini A, Xia JW, Zare R, González CD, Iturriaga T, Savary O, Coton M, Coton E, Jany JL, Liu C, Zeng ZQ, Zhuang WY, Yu ZH, Thines M. Fusarium and allied fusarioid taxa (FUSA). 1. Fungal Syst Evol 2022; 9:161-200. [PMID: 35978986 PMCID: PMC9355104 DOI: 10.3114/fuse.2022.09.08] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/14/2022] [Indexed: 11/07/2022] Open
Abstract
Seven Fusarium species complexes are treated, namely F. aywerte species complex (FASC) (two species), F. buharicum species complex (FBSC) (five species), F. burgessii species complex (FBURSC) (three species), F. camptoceras species complex (FCAMSC) (three species), F. chlamydosporum species complex (FCSC) (eight species), F. citricola species complex (FCCSC) (five species) and the F. concolor species complex (FCOSC) (four species). New species include Fusicolla elongata from soil (Zimbabwe), and Neocosmospora geoasparagicola from soil associated with Asparagus officinalis (Netherlands). New combinations include Neocosmospora akasia, N. awan, N. drepaniformis, N. duplosperma, N. geoasparagicola, N. mekan, N. papillata, N. variasi and N. warna. Newly validated taxa include Longinectria gen. nov., L. lagenoides, L. verticilliforme, Fusicolla gigas and Fusicolla guangxiensis. Furthermore, Fusarium rosicola is reduced to synonymy under N. brevis. Finally, the genome assemblies of Fusarium secorum (CBS 175.32), Microcera coccophila (CBS 310.34), Rectifusarium robinianum (CBS 430.91), Rugonectria rugulosa (CBS 126565), and Thelonectria blattea (CBS 952.68) are also announced here. Citation: Crous PW, Sandoval-Denis M, Costa MM, Groenewald JZ, van Iperen AL, Starink-Willemse M, Hernández-Restrepo M, Kandemir H, Ulaszewski B, de Boer W, Abdel-Azeem AM, Abdollahzadeh J, Akulov A, Bakhshi M, Bezerra JDP, Bhunjun CS, Câmara MPS, Chaverri P, Vieira WAS, Decock CA, Gaya E, Gené J, Guarro J, Gramaje D, Grube M, Gupta VK, Guarnaccia V, Hill R, Hirooka Y, Hyde KD, Jayawardena RS, Jeewon R, Jurjević Ž, Korsten L, Lamprecht SC, Lombard L, Maharachchikumbura SSN, Polizzi G, Rajeshkumar KC, Salgado-Salazar C, Shang Q-J, Shivas RG, Summerbell RC, Sun GY, Swart WJ, Tan YP, Vizzini A, Xia JW, Zare R, González CD, Iturriaga T, Savary O, Coton M, Coton E, Jany J-L, Liu C, Zeng Z-Q, Zhuang W-Y, Yu Z-H, Thines M (2022). Fusarium and allied fusarioid taxa (FUSA). 1. Fungal Systematics and Evolution 9: 161-200. doi: 10.3114/fuse.2022.09.08.
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Affiliation(s)
- P W Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.,Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - M Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M M Costa
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - J Z Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - A L van Iperen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M Starink-Willemse
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M Hernández-Restrepo
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - H Kandemir
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - B Ulaszewski
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - W de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Soil Biology Group, Wageningen University, Wageningen, Netherlands
| | - A M Abdel-Azeem
- Systematic Mycology Lab., Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - J Abdollahzadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - A Akulov
- Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022 Kharkiv, Ukraine
| | - M Bakhshi
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - J D P Bezerra
- Setor de Micologia / Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Rua 235 - s/n - Setor Universitário - CEP: 74605-050, Universidade Federal de Goiás / Federal University of Goiás, Goiânia, Brasil / Goiânia, Brazil
| | - C S Bhunjun
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - M P S Câmara
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - P Chaverri
- Escuela de Biología and Centro de Investigaciones en Productos Naturales, Universidad de Costa Rica, San Pedro, Costa Rica
| | - W A S Vieira
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - C A Decock
- Mycothèque de l'Université catholique de Louvain (MUCL, BCCMTM), Earth and Life Institute - ELIM - Mycology, Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, B-1348 Louvain-la-Neuve, Belgium
| | - E Gaya
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - J Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d'Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201 Reus, Spain
| | - J Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d'Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201 Reus, Spain
| | - D Gramaje
- Institute of Grapevine and Wine Sciences (ICVV), Spanish National Research Council (CSIC)-University of La Rioja-Government of La Rioja, Logroño 26007, Spain
| | - M Grube
- Institut für Biologie, Karl-Franzens-Universität Graz, Holteigasse 6, 8010 Graz, Austria
| | - V K Gupta
- Center for Safe and Improved Food, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.,Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - V Guarnaccia
- Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Torino, Largo P. Braccini 2, 10095 Grugliasco (TO), Italy
| | - R Hill
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - Y Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - K D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - R S Jayawardena
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - R Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit, Mauritius
| | - Ž Jurjević
- EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ 08077, USA
| | - L Korsten
- Department of Plant and Soil Sciences, University of Pretoria, P. Bag X20 Hatfield, Pretoria 0002, South Africa
| | - S C Lamprecht
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch 7599, Western Cape, South Africa
| | - L Lombard
- Dutch General Inspection Service for agricultural seeds and seed potatoes (NAK), Randweg 14, 8304 AS, Emmeloord, The Netherlands
| | - S S N Maharachchikumbura
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, People's Republic of China
| | - G Polizzi
- Dipartimento di Agricoltura, Alimentazione e Ambiente, sez. Patologia vegetale, University of Catania, Via S. Sofia 100, 95123 Catania, Italy
| | - K C Rajeshkumar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) Group, Agharkar Research Institute, Pune, Maharashtra 411 004, India
| | - C Salgado-Salazar
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Bldg. 010A, Rm. 212, BARC-West, 10300 Baltimore Ave. Beltsville, MD 20705, USA
| | - Q-J Shang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, People's Republic of China
| | - R G Shivas
- Centre for Crop Health, University of Southern Queensland, Toowoomba 4350, Queensland, Australia
| | - R C Summerbell
- Sporometrics, Toronto, ON, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - G Y Sun
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - W J Swart
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Y P Tan
- Centre for Crop Health, University of Southern Queensland, Toowoomba 4350, Queensland, Australia.,Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park, Queensland 4102, Australia
| | - A Vizzini
- Department of Life Sciences and Systems Biology, University of Torino and Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R, Viale P.A. Mattioli, 25, I-10125 Torino, Italy
| | - J W Xia
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
| | - R Zare
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - C D González
- Lab. Salud de Bosques, Fac. de Ciencias Forestales y RRNN, Universidad Austral de Chile, Chile
| | - T Iturriaga
- Curator, Cornell University Plant Pathology Herbarium, Ithaca, NY, USA
| | - O Savary
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - M Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - E Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - J-L Jany
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - C Liu
- College of Life Sciences, Yangtze University, Jingzhou, Hubei 434025, China
| | - Z-Q Zeng
- College of Life Sciences, Yangtze University, Jingzhou, Hubei 434025, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - W-Y Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Z-H Yu
- College of Life Sciences, Yangtze University, Jingzhou, Hubei 434025, China
| | - M Thines
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe-University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue Str. 13, D-60438 Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
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12
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Chaverri P, Chaverri G. Fungal communities in feces of the frugivorous bat Ectophylla alba and its highly specialized Ficus colubrinae diet. Anim Microbiome 2022; 4:24. [PMID: 35303964 PMCID: PMC8932179 DOI: 10.1186/s42523-022-00169-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bats are important long-distance dispersers of many tropical plants, yet, by consuming fruits, they may disperse not only the plant's seeds, but also the mycobiota within those fruits. We characterized the culture-dependent and independent fungal communities in fruits of Ficus colubrinae and feces of Ectophylla alba to determine if passage through the digestive tract of bats affected the total mycobiota. RESULTS Using presence/absence and normalized abundance data from fruits and feces, we demonstrate that the fungal communities were significantly different, even though there was an overlap of ca. 38% of Amplicon Sequence Variants (ASVs). We show that some of the fungi from fruits were also present and grew from fecal samples. Fecal fungal communities were dominated by Agaricomycetes, followed by Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Malasseziomycetes, while fruit samples were dominated by Dothideomycetes, followed by Sordariomycetes, Agaricomycetes, Eurotiomycetes, and Laboulbeniomycetes. Linear discriminant analyses (LDA) show that, for bat feces, the indicator taxa include Basidiomycota (i.e., Agaricomycetes: Polyporales and Agaricales), and the ascomycetous class Eurotiomycetes (i.e., Eurotiales, Aspergillaceae). For fruits, indicator taxa are in the Ascomycota (i.e., Dothideomycetes: Botryosphaeriales; Laboulbeniomycetes: Pyxidiophorales; and Sordariomycetes: Glomerellales). In our study, the differences in fungal species composition between the two communities (fruits vs. feces) reflected on the changes in the functional diversity. For example, the core community in bat feces is constituted by saprobes and animal commensals, while that of fruits is composed mostly of phytopathogens and arthropod-associated fungi. CONCLUSIONS Our study provides the groundwork to continue disentangling the direct and indirect symbiotic relationships in an ecological network that has not received enough attention: fungi-plants-bats. Findings also suggest that the role of frugivores in plant-animal mutualistic networks may extend beyond seed dispersal: they may also promote the dispersal of potentially beneficial microbial symbionts while, for example, hindering those that can cause plant disease.
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Affiliation(s)
- Priscila Chaverri
- Escuela de Biología and Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro, Costa Rica. .,Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
| | - Gloriana Chaverri
- Sede del Sur, Universidad de Costa Rica, Golfito, 60701, Costa Rica.,Smithsonian Tropical Research Institute, Balboa, Ancón, Panamá
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13
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Ting ASY, Chaverri P, Edrada-Ebel RA. Editorial: Endophytes and Their Biotechnological Applications. Front Bioeng Biotechnol 2021; 9:795174. [PMID: 34926434 PMCID: PMC8675125 DOI: 10.3389/fbioe.2021.795174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
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14
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Vieto S, Escudero-Leyva E, Avendaño R, Rechnitzer N, Barrantes-Madrigal MD, Conejo-Barboza G, Herrera-Sancho OA, Chaverri P, Chavarría M. Biodeterioration and cellulolytic activity by fungi isolated from a nineteenth-century painting at the National Theatre of Costa Rica. Fungal Biol 2021; 126:101-112. [DOI: 10.1016/j.funbio.2021.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/21/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022]
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15
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Barrera VA, Iannone L, Romero AI, Chaverri P. Expanding the Trichoderma harzianum species complex: Three new species from Argentine natural and cultivated ecosystems. Mycologia 2021; 113:1136-1155. [PMID: 34473608 DOI: 10.1080/00275514.2021.1947641] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A study was performed on a collection of 84 isolates from decaying plant tissues and soils in Argentina previously identified as Trichoderma harzianum. Based on multiple phenotypic characters and multilocus phylogenetic analyses, 10 species were distinguished, three of which are described as new species: T. austroindianum, T. hortense, and T. syagri. Among the remaining seven identified species, the following five can be added to the Argentine mycobiota: T. afarasin, T. afroharzianum, T. endophyticum, T. guizhouense, and T. neotropicale. Trichoderma afroharzianum and T. endophyticum were the most frequent species found in the samples. In addition, a collection of isolates previously identified as T. harzianum with antagonistic abilities were reidentified as T. afroharzianum, thus highlighting the importance of correct identification of biocontrol species.
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Affiliation(s)
- Viviana A Barrera
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola, N. Repetto y De los Reseros, CC25 (1712), Castelar, Buenos Aires, Argentina
| | - Leopoldo Iannone
- Instituto de Micología y Botánica-Consejo Nacional de Investigaciones Científicas y Técnicas (INMIBO-CONICET), Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Av. Int. Güiraldes 2620, Buenos Aires C1428EHA, Argentina
| | - Andrea Irene Romero
- Instituto de Micología y Botánica-Consejo Nacional de Investigaciones Científicas y Técnicas (INMIBO-CONICET), Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Av. Int. Güiraldes 2620, Buenos Aires C1428EHA, Argentina
| | - Priscila Chaverri
- Escuela de Biología and Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro, San José, Costa Rica.,Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742
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16
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Crous P, Lombard L, Sandoval-Denis M, Seifert K, Schroers HJ, Chaverri P, Gené J, Guarro J, Hirooka Y, Bensch K, Kema G, Lamprecht S, Cai L, Rossman A, Stadler M, Summerbell R, Taylor J, Ploch S, Visagie C, Yilmaz N, Frisvad J, Abdel-Azeem A, Abdollahzadeh J, Abdolrasouli A, Akulov A, Alberts J, Araújo J, Ariyawansa H, Bakhshi M, Bendiksby M, Ben Hadj Amor A, Bezerra J, Boekhout T, Câmara M, Carbia M, Cardinali G, Castañeda-Ruiz R, Celis A, Chaturvedi V, Collemare J, Croll D, Damm U, Decock C, de Vries R, Ezekiel C, Fan X, Fernández N, Gaya E, González C, Gramaje D, Groenewald J, Grube M, Guevara-Suarez M, Gupta V, Guarnaccia V, Haddaji A, Hagen F, Haelewaters D, Hansen K, Hashimoto A, Hernández-Restrepo M, Houbraken J, Hubka V, Hyde K, Iturriaga T, Jeewon R, Johnston P, Jurjević Ž, Karalti İ, Korsten L, Kuramae E, Kušan I, Labuda R, Lawrence D, Lee H, Lechat C, Li H, Litovka Y, Maharachchikumbura S, Marin-Felix Y, Matio Kemkuignou B, Matočec N, McTaggart A, Mlčoch P, Mugnai L, Nakashima C, Nilsson R, Noumeur S, Pavlov I, Peralta M, Phillips A, Pitt J, Polizzi G, Quaedvlieg W, Rajeshkumar K, Restrepo S, Rhaiem A, Robert J, Robert V, Rodrigues A, Salgado-Salazar C, Samson R, Santos A, Shivas R, Souza-Motta C, Sun G, Swart W, Szoke S, Tan Y, Taylor J, Taylor P, Tiago P, Váczy K, van de Wiele N, van der Merwe N, Verkley G, Vieira W, Vizzini A, Weir B, Wijayawardene N, Xia J, Yáñez-Morales M, Yurkov A, Zamora J, Zare R, Zhang C, Thines M. Fusarium: more than a node or a foot-shaped basal cell. Stud Mycol 2021; 98:100116. [PMID: 34466168 PMCID: PMC8379525 DOI: 10.1016/j.simyco.2021.100116] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
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Key Words
- Apiognomonia platani (Lév.) L. Lombard
- Atractium ciliatum Link
- Atractium pallidum Bonord.
- Calloria tremelloides (Grev.) L. Lombard
- Cephalosporium sacchari E.J. Butler
- Cosmosporella cavisperma (Corda) Sand.-Den., L. Lombard & Crous
- Cylindrodendrum orthosporum (Sacc. & P. Syd.) L. Lombard
- Dialonectria volutella (Ellis & Everh.) L. Lombard & Sand.-Den.
- Fusarium aeruginosum Delacr.
- Fusarium agaricorum Sarrazin
- Fusarium albidoviolaceum Dasz.
- Fusarium aleyrodis Petch
- Fusarium amentorum Lacroix
- Fusarium annuum Leonian
- Fusarium arcuatum Berk. & M.A. Curtis
- Fusarium aridum O.A. Pratt
- Fusarium armeniacum (G.A. Forbes et al.) L.W. Burgess & Summerell
- Fusarium arthrosporioides Sherb.
- Fusarium asparagi Delacr.
- Fusarium batatas Wollenw.
- Fusarium biforme Sherb.
- Fusarium buharicum Jacz. ex Babajan & Teterevn.-Babajan
- Fusarium cactacearum Pasin. & Buzz.-Trav.
- Fusarium cacti-maxonii Pasin. & Buzz.-Trav.
- Fusarium caudatum Wollenw.
- Fusarium cavispermum Corda
- Fusarium cepae Hanzawa
- Fusarium cesatii Rabenh.
- Fusarium citriforme Jamal.
- Fusarium citrinum Wollenw.
- Fusarium citrulli Taubenh.
- Fusarium clavatum Sherb.
- Fusarium coccinellum Kalchbr.
- Fusarium cromyophthoron Sideris
- Fusarium cucurbitae Taubenh.
- Fusarium cuneiforme Sherb.
- Fusarium delacroixii Sacc.
- Fusarium dimerum var. nectrioides Wollenw.
- Fusarium echinatum Sand.-Den. & G.J. Marais
- Fusarium epicoccum McAlpine
- Fusarium eucheliae Sartory, R. Sartory & J. Mey.
- Fusarium fissum Peyl
- Fusarium flocciferum Corda
- Fusarium gemmiperda Aderh.
- Fusarium genevense Dasz.
- Fusarium graminearum Schwabe
- Fusarium graminum Corda
- Fusarium heterosporioides Fautrey
- Fusarium heterosporum Nees & T. Nees
- Fusarium idahoanum O.A. Pratt
- Fusarium juruanum Henn.
- Fusarium lanceolatum O.A. Pratt
- Fusarium lateritium Nees
- Fusarium loncheceras Sideris
- Fusarium longipes Wollenw. & Reinking
- Fusarium lyarnte J.L. Walsh, Sangal., L.W. Burgess, E.C.Y. Liew & Summerell
- Fusarium malvacearum Taubenh.
- Fusarium martii f. phaseoli Burkh.
- Fusarium muentzii Delacr.
- Fusarium nigrum O.A. Pratt
- Fusarium oxysporum var. asclerotium Sherb.
- Fusarium palczewskii Jacz.
- Fusarium palustre W.H. Elmer & Marra
- Fusarium polymorphum Matr.
- Fusarium poolense Taubenh.
- Fusarium prieskaense G.J. Marais & Sand.-Den.
- Fusarium prunorum McAlpine
- Fusarium pusillum Wollenw.
- Fusarium putrefaciens Osterw.
- Fusarium redolens Wollenw.
- Fusarium reticulatum Mont.
- Fusarium rhizochromatistes Sideris
- Fusarium rhizophilum Corda
- Fusarium rhodellum McAlpine
- Fusarium roesleri Thüm.
- Fusarium rostratum Appel & Wollenw.
- Fusarium rubiginosum Appel & Wollenw.
- Fusarium rubrum Parav.
- Fusarium samoense Gehrm.
- Fusarium scirpi Lambotte & Fautrey
- Fusarium secalis Jacz.
- Fusarium spinaciae Hungerf.
- Fusarium sporotrichioides Sherb.
- Fusarium stercoris Fuckel
- Fusarium stilboides Wollenw.
- Fusarium stillatum De Not. ex Sacc.
- Fusarium sublunatum Reinking
- Fusarium succisae Schröt. ex Sacc.
- Fusarium tabacivorum Delacr.
- Fusarium trichothecioides Wollenw.
- Fusarium tritici Liebman
- Fusarium tuberivorum Wilcox & G.K. Link
- Fusarium tumidum var. humi Reinking
- Fusarium ustilaginis Kellerm. & Swingle
- Fusarium viticola Thüm.
- Fusarium werrikimbe J.L. Walsh, L.W. Burgess, E.C.Y. Liew & B.A. Summerell
- Fusarium willkommii Lindau
- Fusarium xylarioides Steyaert
- Fusarium zygopetali Delacr.
- Fusicolla meniscoidea L. Lombard & Sand.-Den.
- Fusicolla quarantenae J.D.P. Bezerra, Sand.-Den., Crous & Souza-Motta
- Fusicolla sporellula Sand.-Den. & L. Lombard
- Fusisporium andropogonis Cooke ex Thüm.
- Fusisporium anthophilum A. Braun
- Fusisporium arundinis Corda
- Fusisporium avenaceum Fr.
- Fusisporium clypeaster Corda
- Fusisporium culmorum Wm.G. Sm.
- Fusisporium didymum Harting
- Fusisporium elasticae Thüm.
- Fusisporium episphaericum Cooke & Ellis
- Fusisporium flavidum Bonord.
- Fusisporium hordei Wm.G. Sm.
- Fusisporium incarnatum Roberge ex Desm.
- Fusisporium lolii Wm.G. Sm.
- Fusisporium pandani Corda
- Gibberella phyllostachydicola W. Yamam.
- Hymenella aurea (Corda) L. Lombard
- Hymenella spermogoniopsis (Jul. Müll.) L. Lombard & Sand.-Den.
- Luteonectria Sand.-Den., L. Lombard, Schroers & Rossman
- Luteonectria albida (Rossman) Sand.-Den. & L. Lombard
- Luteonectria nematophila (Nirenberg & Hagedorn) Sand.-Den. & L. Lombard
- Macroconia bulbipes Crous & Sand.-Den.
- Macroconia phlogioides Sand.-Den. & Crous
- Menispora penicillata Harz
- Multi-gene phylogeny
- Mycotoxins
- Nectriaceae
- Neocosmospora
- Neocosmospora epipeda Quaedvl. & Sand.-Den.
- Neocosmospora floridana (T. Aoki et al.) L. Lombard & Sand.-Den.
- Neocosmospora merkxiana Quaedvl. & Sand.-Den.
- Neocosmospora neerlandica Crous & Sand.-Den.
- Neocosmospora nelsonii Crous & Sand.-Den.
- Neocosmospora obliquiseptata (T. Aoki et al.) L. Lombard & Sand.-Den.
- Neocosmospora pseudopisi Sand.-Den. & L. Lombard
- Neocosmospora rekana (Lynn & Marinc.) L. Lombard & Sand.-Den.
- Neocosmospora tuaranensis (T. Aoki et al.) L. Lombard & Sand.-Den.
- Nothofusarium Crous, Sand.-Den. & L. Lombard
- Nothofusarium devonianum L. Lombard, Crous & Sand.-Den.
- Novel taxa
- Pathogen
- Scolecofusarium L. Lombard, Sand.-Den. & Crous
- Scolecofusarium ciliatum (Link) L. Lombard, Sand.-Den. & Crous
- Selenosporium equiseti Corda
- Selenosporium hippocastani Corda
- Selenosporium sarcochroum Desm
- Selenosporium urticearum Corda.
- Setofusarium (Nirenberg & Samuels) Crous & Sand.-Den.
- Setofusarium setosum (Samuels & Nirenberg) Sand.-Den. & Crous.
- Sphaeria sanguinea var. cicatricum Berk.
- Sporotrichum poae Peck.
- Stylonectria corniculata Gräfenhan, Crous & Sand.-Den.
- Stylonectria hetmanica Akulov, Crous & Sand.-Den.
- Taxonomy
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Affiliation(s)
- P.W. Crous
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - L. Lombard
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - K.A. Seifert
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - H.-J. Schroers
- Plant Protection Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000, Ljubljana, Slovenia
| | - P. Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
- Escuela de Biología and Centro de Investigaciones en Productos Naturales, Universidad de Costa Rica, San Pedro, Costa Rica
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201, Reus, Spain
| | - J. Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201, Reus, Spain
| | - Y. Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo, 184-8584, Japan
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - G.H.J. Kema
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - S.C. Lamprecht
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, Western Cape, South Africa
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - A.Y. Rossman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, 97330, USA
| | - M. Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - R.C. Summerbell
- Sporometrics, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - J.W. Taylor
- Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA, 94720-3102, USA
| | - S. Ploch
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, DTU-Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - A.M. Abdel-Azeem
- Systematic Mycology Lab., Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - J. Abdollahzadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - A. Abdolrasouli
- Department of Medical Microbiology, King's College Hospital, London, UK
- Department of Infectious Diseases, Imperial College London, London, UK
| | - A. Akulov
- Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022, Kharkiv, Ukraine
| | - J.F. Alberts
- Department of Food Science and Technology, Cape Peninsula University of Technology, P.O. Box 1906, Bellville, 7535, South Africa
| | - J.P.M. Araújo
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - H.A. Ariyawansa
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 106, Taiwan, ROC
| | - M. Bakhshi
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - M. Bendiksby
- Natural History Museum, University of Oslo, Norway
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - A. Ben Hadj Amor
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - J.D.P. Bezerra
- Setor de Micologia/Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Rua 235 - s/n – Setor Universitário - CEP: 74605-050, Universidade Federal de Goiás/Federal University of Goiás, Goiânia, Brazil
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M.P.S. Câmara
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - M. Carbia
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina – Universidad de la República, Av. A. Navarro 3051, Montevideo, Uruguay
| | - G. Cardinali
- Department of Pharmaceutical Science, University of Perugia, Via Borgo 20 Giugno, 74 Perugia, Italy
| | - R.F. Castañeda-Ruiz
- Instituto de Investigaciones Fundamentales en Agricultura Tropical Alejandro de Humboldt (INIFAT), Académico Titular de la Academia de Ciencias de, Cuba
| | - A. Celis
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, 111711, Colombia
| | - V. Chaturvedi
- Mycology Laboratory, New York State Department of Health Wadsworth Center, Albany, NY, USA
| | - J. Collemare
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - D. Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, CH-2000, Neuchatel, Switzerland
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806, Görlitz, Germany
| | - C.A. Decock
- Mycothèque de l'Université catholique de Louvain (MUCL, BCCMTM), Earth and Life Institute – ELIM – Mycology, Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, B-1348, Louvain-la-Neuve, Belgium
| | - R.P. de Vries
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - C.N. Ezekiel
- Department of Microbiology, Babcock University, Ilishan Remo, Ogun State, Nigeria
| | - X.L. Fan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - N.B. Fernández
- Laboratorio de Micología Clínica, Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - E. Gaya
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - C.D. González
- Laboratorio de Salud de Bosques y Ecosistemas, Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, casilla 567, Valdivia, Chile
| | - D. Gramaje
- Institute of Grapevine and Wine Sciences (ICVV), Spanish National Research Council (CSIC)-University of La Rioja-Government of La Rioja, Logroño, 26007, Spain
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M. Grube
- Institut für Biologie, Karl-Franzens-Universität Graz, Holteigasse 6, 8010, Graz, Austria
| | - M. Guevara-Suarez
- Applied genomics research group, Universidad de los Andes, Cr 1 # 18 a 12, Bogotá, Colombia
| | - V.K. Gupta
- Center for Safe and Improved Food, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - V. Guarnaccia
- Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Torino, Largo P. Braccini 2, 10095, Grugliasco, TO, Italy
| | | | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - D. Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, 35 K.L. Ledeganckstraat, 9000, Ghent, Belgium
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - K. Hansen
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - A. Hashimoto
- Microbe Division/Japan Collection of Microorganisms RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | | | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - V. Hubka
- Department of Botany, Charles University in Prague, Prague, Czech Republic
| | - K.D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chaing Rai, 57100, Thailand
| | - T. Iturriaga
- Cornell University, 334 Plant Science Building, Ithaca, NY, 14850, USA
| | - R. Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit, Mauritius
| | - P.R. Johnston
- Manaaki Whenua Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Ž. Jurjević
- EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ, 08077, USA
| | - İ. Karalti
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Yeditepe University, Turkey
| | - L. Korsten
- Department of Plant and Soil Sciences, University of Pretoria, P. Bag X20 Hatfield, Pretoria, 0002, South Africa
| | - E.E. Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
- Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - I. Kušan
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - R. Labuda
- University of Veterinary Medicine, Vienna (VetMed), Institute of Food Safety, Food Technology and Veterinary Public Health, Veterinaerplatz 1, 1210 Vienna and BiMM – Bioactive Microbial Metabolites group, 3430 Tulln a.d. Donau, Austria
| | - D.P. Lawrence
- University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - H.B. Lee
- Department of Agricultural Biological Chemistry, College of Agriculture & Life Sciences, Chonnam National University, Yongbong-Dong 300, Buk-Gu, Gwangju, 61186, South Korea
| | - C. Lechat
- Ascofrance, 64 route de Chizé, 79360, Villiers-en-Bois, France
| | - H.Y. Li
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Y.A. Litovka
- V.N. Sukachev Institute of Forest SB RAS, Laboratory of Reforestation, Mycology and Plant Pathology, Krasnoyarsk, 660036, Russia
- Reshetnev Siberian State University of Science and Technology, Department of Chemical Technology of Wood and Biotechnology, Krasnoyarsk, 660037, Russia
| | - S.S.N. Maharachchikumbura
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Y. Marin-Felix
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - B. Matio Kemkuignou
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - N. Matočec
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - A.R. McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, G.P.O. Box 267, Brisbane, 4001, Australia
| | - P. Mlčoch
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - L. Mugnai
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology section, University of Florence, P.le delle Cascine 28, 50144, Firenze, Italy
| | - C. Nakashima
- Graduate school of Bioresources, Mie University, Kurima-machiya 1577, Tsu, Mie, 514-8507, Japan
| | - R.H. Nilsson
- Gothenburg Global Biodiversity Center at the Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
| | - S.R. Noumeur
- Department of Microbiology and Biochemistry, Faculty of Natural and Life Sciences, University of Batna 2, Batna, 05000, Algeria
| | - I.N. Pavlov
- V.N. Sukachev Institute of Forest SB RAS, Laboratory of Reforestation, Mycology and Plant Pathology, Krasnoyarsk, 660036, Russia
- Reshetnev Siberian State University of Science and Technology, Department of Chemical Technology of Wood and Biotechnology, Krasnoyarsk, 660037, Russia
| | - M.P. Peralta
- Laboratorio de Micodiversidad y Micoprospección, PROIMI-CONICET, Av. Belgrano y Pje. Caseros, Argentina
| | - A.J.L. Phillips
- Universidade de Lisboa, Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Campo Grande, 1749-016, Lisbon, Portugal
| | - J.I. Pitt
- Microbial Screening Technologies, 28 Percival Rd, Smithfield, NSW, 2164, Australia
| | - G. Polizzi
- Dipartimento di Agricoltura, Alimentazione e Ambiente, sez. Patologia vegetale, University of Catania, Via S. Sofia 100, 95123 Catania, Italy
| | - W. Quaedvlieg
- Phytopathology, Van Zanten Breeding B.V., Lavendelweg 15, 1435 EW, Rijsenhout, the Netherlands
| | - K.C. Rajeshkumar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) Group, Agharkar Research Institute, Pune, Maharashtra, 411 004, India
| | - S. Restrepo
- Laboratory of Mycology and Phytopathology – (LAMFU), Department of Chemical and Food Engineering, Universidad de los Andes, Cr 1 # 18 a 12, Bogotá, Colombia
| | - A. Rhaiem
- Plant Pathology and Population Genetics, Laboratory of Microorganisms, National Gene Bank, Tunisia
| | | | - V. Robert
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - C. Salgado-Salazar
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Bldg. 010A, Rm. 212, BARC-West, 10300 Baltimore Ave, Beltsville, MD, 20705, USA
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - A.C.S. Santos
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - R.G. Shivas
- Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, Queensland, Australia
| | - C.M. Souza-Motta
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - G.Y. Sun
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - W.J. Swart
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | | | - Y.P. Tan
- Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, Queensland, Australia
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park, Queensland, 4102, Australia
| | - J.E. Taylor
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, United Kingdom
| | - P.W.J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - P.V. Tiago
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - K.Z. Váczy
- Food and Wine Research Institute, Eszterházy Károly University, 6 Leányka Street, H-3300, Eger, Hungary
| | | | - N.A. van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - G.J.M. Verkley
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - W.A.S. Vieira
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - A. Vizzini
- Department of Life Sciences and Systems Biology, University of Torino and Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R, Viale P.A. Mattioli, 25, I-10125, Torino, Italy
| | - B.S. Weir
- Manaaki Whenua Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - N.N. Wijayawardene
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - J.W. Xia
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
| | - M.J. Yáñez-Morales
- Fitosanidad, Colegio de Postgraduados-Campus Montecillo, Montecillo-Texcoco, 56230 Edo. de Mexico, Mexico
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, SE-752 36, Uppsala, Sweden
| | - R. Zare
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - C.L. Zhang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, China
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
- Goethe-University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue Str. 13, D-60438, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
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Seas C, Chaverri P. Response of psychrophilic plant endosymbionts to experimental temperature increase. R Soc Open Sci 2020; 7:201405. [PMID: 33489283 PMCID: PMC7813268 DOI: 10.1098/rsos.201405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Countless uncertainties remain regarding the effects of global warming on biodiversity, including the ability of organisms to adapt and how that will affect obligate symbiotic relationships. The present study aimed to determine the consequences of temperature increase in the adaptation of plant endosymbionts (endophytes) that grow better at low temperatures (psychrophilic). We isolated fungal endophytes from a high-elevation (paramo) endemic plant, Chusquea subtessellata. Initial growth curves were constructed at different temperatures (4-25°C). Next, experiments were carried out in which only the psychrophilic isolates were subjected to repeated increments in temperature. After the experiments, the final growth curves showed significantly slower growth than the initial curves, and some isolates even ceased to grow. While most studies suggest that the distribution of microorganisms will expand as temperatures increase because most of these organisms grow better at 25°C, the results from our experiments demonstrate that psychrophilic fungi were negatively affected by temperature increases. These outcomes raise questions concerning the potential adaptation of beneficial endosymbiotic fungi in the already threatened high-elevation ecosystems. Assessing the consequences of global warming at all trophic levels is urgent because many species on Earth depend on their microbial symbionts for survival.
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Affiliation(s)
- Carolina Seas
- Vicerrectoría de Investigación, Laboratorio de Ecología Urbana, Universidad Estatal a Distancia (UNED), 2050 San José, Costa Rica
- Centro Agronómico Tropical de Investigación y Enseñanza (CATIE), Escuela de Posgrado, Turrialba, Costa Rica
| | - Priscila Chaverri
- Escuela de Biología and Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
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Silva RAFD, de Almeida CP, Reis A, Aguiar FM, Chaverri P, Pinho DB. Three new species of Gliocephalotrichum causing fruit rot on different hosts from Brazil. Mycologia 2020; 112:1003-1016. [PMID: 32946336 DOI: 10.1080/00275514.2020.1801017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The genus Gliocephalotrichum (Nectriaceae), originally described as a soil-borne fungus, has been associated with postharvest diseases, especially of tropical fruits. Taxonomic studies using both morphological and molecular phylogenetic analyses have contributed to recognition of novel species in several countries. However, in Brazil, only three isolates of Gliocephalotrichum have been collected from soil samples and roots since the late 1970s. Our study expands the sample range using many Gliocephalotrichum isolates obtained from rotting fruits of tropical plant species in different states of Brazil. Polyphasic taxonomy was assessed with phylogenetic analyses of DNA sequences from four nuclear loci, morphological comparisons, and pathogenicity tests. As a result, three known species (G. bulbilium, G. longibrachium, and G. simplex) were identified from new hosts and locations in Brazil. In addition, three new species are described-G. abrachium, G. brasiliense, and G. caryocaris. A key to all Gliocephalotrichum species worldwide is provided. Although species of Gliocephalotrichum have not been considered to be important plant pathogens, this study shows they may cause postharvest fruit rot in tropical fruits and therefore have an impact in communities that depend economically on the harvest and sale of these fruits.
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Affiliation(s)
| | - Camila Pereira de Almeida
- Departamento de Fitopatologia, Universidade de Brasília , Brasília, Distrito Federal, 70910-900, Brazil
| | - Ailton Reis
- Empresa Brasileira de Pesquisas Agropecuárias (EMBRAPA)-Hortaliças , 70275-970, Brasília, Distrito Federal, Brazil
| | - Frederick Mendes Aguiar
- Departamento de Fitopatologia, Universidade de Brasília , Brasília, Distrito Federal, 70910-900, Brazil
| | - Priscila Chaverri
- Escuela de Biología and Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica , San Pedro, San José, Costa Rica
| | - Danilo Batista Pinho
- Departamento de Fitopatologia, Universidade de Brasília , Brasília, Distrito Federal, 70910-900, Brazil
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Montero-Vargas M, Escudero-Leyva E, Díaz-Valerio S, Chaverri P. Step-by-Step Pipeline for the Ecological Analysis of Endophytic Fungi using ITS nrDNA Data. ACTA ACUST UNITED AC 2020; 56:e96. [PMID: 31910332 DOI: 10.1002/cpmc.96] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The nuclear ribosomal DNA internal transcribed spacer (ITS) is accepted as the genetic marker or barcode of choice for the identification of fungal samples. Here, we present a protocol to analyze fungal ITS data, from quality preprocessing of raw sequences to identification of operational taxonomic units (OTUs), taxonomic classification, and assignment of functional traits. The pipeline relies on well-established and manually curated data collections, namely the UNITE database and the FUNGuild script. As an example, real ITS data from culturable endophytic fungi were analyzed, providing detailed descriptions for every step, parameter, and downstream analysis, and finishing with a phylogenetic analysis of the sequences and assigned ecological roles. This article constitutes a comprehensive guide for researchers that have little familiarity with bioinformatic analysis of essential steps required in further ecological studies of fungal communities. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Raw sequencing data processing Support Protocol: Building a BLAST database Basic Protocol 2: Obtaining information from databases Basic Protocol 3: Phylogenetic analysis.
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Affiliation(s)
- Maripaz Montero-Vargas
- Colaboratorio Nacional de Computación Avanzada (CNCA), CeNAT-CONARE, San José, Costa Rica
| | - Efraín Escudero-Leyva
- Escuela de Biología and Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica.,Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Stefani Díaz-Valerio
- Colaboratorio Nacional de Computación Avanzada (CNCA), CeNAT-CONARE, San José, Costa Rica
| | - Priscila Chaverri
- Escuela de Biología and Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica.,Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland
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Pujade-Renaud V, Déon M, Gazis R, Ribeiro S, Dessailly F, Granet F, Chaverri P. Endophytes from Wild Rubber Trees as Antagonists of the Pathogen Corynespora cassiicola. Phytopathology 2019; 109:1888-1899. [PMID: 31290729 DOI: 10.1094/phyto-03-19-0093-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Corynespora leaf fall disease of rubber trees, caused by the necrotrophic fungus Corynespora cassiicola, is responsible for important yield losses in Asian and African plantations, whereas its impact is negligible in South America. The objective of this study was to identify potential antagonists of C. cassiicola among fungal endophytes (i.e., Pestalotiopsis, Colletotrichum, and Trichoderma spp.) isolated from wild and cultivated rubber trees distributed in the Peruvian Amazon. We first tested the endophytes in dual in vitro confrontation assays against a virulent C. cassiicola isolate (CCP) obtained from diseased rubber trees in the Philippines. All Trichoderma isolates overran the CCP colony, suggesting some antagonistic mechanism, while species from the other genera behaved as mutual antagonists. Trichoderma isolates were then tested through antibiosis assays for their capacity to produce growth-inhibiting molecules. One isolate (LA279), recovered as an endophyte from a wild Hevea guianensis specimen and identified as Trichoderma koningiopsis, showed significant antibiosis capacity. We demonstrated that LA279 was also able to endophytically colonize the cultivated rubber tree species (H. brasiliensis). Under controlled laboratory conditions, rubber plants were inoculated with three Trichoderma strains, including LA279, in combination with the pathogenic CCP. Results showed that 1 week preinoculation with the endophytes differentially reduced CCP mycelial development and symptoms. In conclusion, this study suggests that T. koningiopsis isolate LA279-and derivate compounds-could be a promising candidate for the biological control of the important rubber tree pathogen C. cassiicola.
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Affiliation(s)
- Valérie Pujade-Renaud
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, UMR PIAF, Clermont-Ferrand, France
- CIRAD, UMR AGAP, F-63000 Clermont-Ferrand, France
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Marine Déon
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, UMR PIAF, Clermont-Ferrand, France
- CIRAD, UMR AGAP, F-63000 Clermont-Ferrand, France
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Romina Gazis
- Tropical Research and Education Center, Department of Plant Pathology, University of Florida, Homestead, FL 33031, U.S.A
| | - Sébastien Ribeiro
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, UMR PIAF, Clermont-Ferrand, France
- CIRAD, UMR AGAP, F-63000 Clermont-Ferrand, France
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Florence Dessailly
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Françoise Granet
- Manufacture Française des Pneumatiques MICHELIN, Place des Carmes-Déchaux, Clermont-Ferrand Cedex, France
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, University of Maryland, College Park, MD 20742, U.S.A
- Escuela de Biología and Centro de Investigación en Productos Naturales, Universidad de Costa Rica, San Pedro, San José, Costa Rica
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Skaltsas DN, Badotti F, Vaz ABM, Silva FFD, Gazis R, Wurdack K, Castlebury L, Góes-Neto A, Chaverri P. Exploration of stem endophytic communities revealed developmental stage as one of the drivers of fungal endophytic community assemblages in two Amazonian hardwood genera. Sci Rep 2019; 9:12685. [PMID: 31481728 PMCID: PMC6722055 DOI: 10.1038/s41598-019-48943-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Many aspects of the dynamics of tropical fungal endophyte communities are poorly known, including the influence of host taxonomy, host life stage, host defence, and host geographical distance on community assembly and composition. Recent fungal endophyte research has focused on Hevea brasiliensis due to its global importance as the main source of natural rubber. However, almost no data exist on the fungal community harboured within other Hevea species or its sister genus Micrandra. In this study, we expanded sampling to include four additional Hevea spp. and two Micrandra spp., as well as two host developmental stages. Through culture-dependent and -independent (metagenomic) approaches, a total of 381 seedlings and 144 adults distributed across three remote areas within the Peruvian Amazon were sampled. Results from both sampling methodologies indicate that host developmental stage had a greater influence in community assemblage than host taxonomy or locality. Based on FunGuild ecological guild assignments, saprotrophic and mycotrophic endophytes were more frequent in adults, while plant pathogens were dominant in seedlings. Trichoderma was the most abundant genus recovered from adult trees while Diaporthe prevailed in seedlings. Potential explanations for that disparity of abundance are discussed in relation to plant physiological traits and community ecology hypotheses.
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Affiliation(s)
- Demetra N Skaltsas
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland, 20742, USA.
- U.S. Department of Agriculture, Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland, 20705, USA.
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, MC-100-44, Oak Ridge, TN, 37831, USA.
| | - Fernanda Badotti
- Centro Federal de Educação Tecnológica de Minas Gerais, Departamento de Química, 30421-169, Belo Horizonte, Minas Gerais, 30421-169, Brazil
| | - Aline Bruna Martins Vaz
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, 31270-901, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Felipe Ferreira da Silva
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, 31270-901, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Romina Gazis
- University of Florida, Department of Plant Pathology, Tropical Research & Education Center, 18905 SW 280 Street, Homestead, Florida, 33031, USA
| | - Kenneth Wurdack
- Smithsonian Institution, Department of Botany, National Museum of Natural History, P.O. Box 37012, Washington, District of Columbia, 20013, USA
| | - Lisa Castlebury
- U.S. Department of Agriculture, Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland, 20705, USA
| | - Aristóteles Góes-Neto
- Centro Federal de Educação Tecnológica de Minas Gerais, Departamento de Química, 30421-169, Belo Horizonte, Minas Gerais, 30421-169, Brazil
| | - Priscila Chaverri
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland, 20742, USA
- Escuela de Biología, Centro de Investigaciones en Productos Naturales, Universidad de Costa Rica, San Pedro, San José, 11501, Costa Rica, USA
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22
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Affiliation(s)
- Priscila Chaverri
- United States Department of Agriculture, Agricultural Research Service, Systematic Botany and Mycology Lab., Rm. 304, B-011A, BARC-W, Beltsville, Maryland 20705-2350
| | - Gary J. Samuels
- United States Department of Agriculture, Agricultural Research Service, Systematic Botany and Mycology Lab., Rm. 304, B-011A, BARC-W, Beltsville, Maryland 20705-2350
| | - Elwin L. Stewart
- The Pennsylvania State University, Department of Plant Pathology, 212 Buckhout Lab., University Park, Pennsylvania 16802
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23
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Fonseca PLC, Badotti F, de Oliveira TFP, Fonseca A, Vaz ABM, Tomé LMR, Abrahão JS, Marques JT, Trindade GS, Chaverri P, Aguiar ERGR, Góes-Neto A. Virome analyses of Hevea brasiliensis using small RNA deep sequencing and PCR techniques reveal the presence of a potential new virus. Virol J 2018; 15:184. [PMID: 30477549 PMCID: PMC6258436 DOI: 10.1186/s12985-018-1095-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/16/2018] [Indexed: 11/10/2022] Open
Abstract
Background Hevea brasiliensis is an important commercial crop due to the high quality of the latex it produces; however, little is known about viral infections in this plant. The only virus described to infect H. brasiliensis until now is a Carlavirus, which was described more than 30 years ago. Virus-derived small interfering RNA (vsiRNAs) are the product of the plant’s antiviral defense triggered by dsRNA viral intermediates generated, during the replication cycle. These vsiRNAs are complementar to viral genomes and have been widely used to identify and characterize viruses in plants. Methods In the present study, we investigated the virome of leaf and sapwood samples from native H. brasiliensis trees collected in two geographic areas in the Brazilian Amazon. Small RNA (sRNA) deep sequencing and bioinformatic tools were used to assembly, identify and characterize viral contigs. Subsequently, PCR amplification techniques were performed to experimentally verify the presence of the viral sequences. Finally, the phylogenetic relationship of the putative new virus with related viral genomes was analyzed. Results Our strategy allowed the identification of 32 contigs with high similarity to viral reference genomes, from which 23 exhibited homology to viruses of the Tymoviridae family. The reads showed a predominant size distribution at 21 nt derived from both strands, which was consistent with the vsiRNAs profile. The presence and genome position of the viral contigs were experimentally confirmed using droplet digital PCR amplifications. A 1913 aa long fragment was obtained and used to infer the phylogenetic relationship of the putative new virus, which indicated that it is taxonomically related to the Grapevine fleck virus, genus Maculavirus. The putative new virus was named Hevea brasiliensis virus (HBrV) in reference to its host. Conclusion The methodological strategy applied here proved to be efficient in detecting and confirming the presence of new viral sequences on a ‘very difficult to manage’ sample. This is the second time that viral sequences, that could be ascribed as a putative novel virus, associated to the rubber tree has been identified. Electronic supplementary material The online version of this article (10.1186/s12985-018-1095-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paula L C Fonseca
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Belo Horizonte, MG, 30421-169, Brazil
| | - Tatiana F P de Oliveira
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.,LANAGRO/MG -Laboratório Nacional da Agricultura, Ministério da Agricultura (MAPA), Pedro Leopoldo, MG, 33600-000, Brazil
| | - Antônio Fonseca
- LANAGRO/MG -Laboratório Nacional da Agricultura, Ministério da Agricultura (MAPA), Pedro Leopoldo, MG, 33600-000, Brazil
| | - Aline B M Vaz
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.,Faculdade de Minas (FAMINAS), Belo Horizonte, MG, 31744-007, Brazil
| | - Luiz M R Tomé
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Jônatas S Abrahão
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - João T Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Giliane S Trindade
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.,Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, 11501-2060, Costa Rica
| | - Eric R G R Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil. .,Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, BA, ,40110-100, Brazil.
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.
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24
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Coronado-Ruiz C, Avendaño R, Escudero-Leyva E, Conejo-Barboza G, Chaverri P, Chavarría M. Two new cellulolytic fungal species isolated from a 19 th-century art collection. Sci Rep 2018; 8:7492. [PMID: 29748544 PMCID: PMC5945893 DOI: 10.1038/s41598-018-24934-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 04/12/2018] [Indexed: 11/08/2022] Open
Abstract
The archive of the Universidad de Costa Rica maintains a nineteenth-century French collection of drawings and lithographs in which the biodeterioration by fungi is rampant. Because of nutritional conditions in which these fungi grew, we suspected that they possessed an ability to degrade cellulose. In this work our goal was to isolate and identify the fungal species responsible for the biodegradation of a nineteenth-century art collection and determine their cellulolytic activity. Fungi were isolated using potato-dextrose-agar (PDA) and water-agar with carboxymethyl cellulose (CMC). The identification of the fungi was assessed through DNA sequencing (nrDNA ITS and α-actin regions) complemented with morphological analyses. Assays for cellulolytic activity were conducted with Gram's iodine as dye. Nineteen isolates were obtained, of which seventeen were identified through DNA sequencing to species level, belonging mainly to genera Arthrinium, Aspergillus, Chaetomium, Cladosporium, Colletotrichum, Penicillium and Trichoderma. For two samples that could not be identified through their ITS and α-actin sequences, a morphological analysis was conducted; they were identified as new species, named Periconia epilithographicola sp. nov. and Coniochaeta cipronana sp. nov. Qualitative tests showed that the fungal collection presents important cellulolytic activity.
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Affiliation(s)
- Carolina Coronado-Ruiz
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San Jose, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San Jose, Costa Rica
| | - Efraín Escudero-Leyva
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
| | - Geraldine Conejo-Barboza
- Escuela de Química, Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
- Instituto de Investigaciones en Arte (II Arte), 11501-2060, San Jose, Costa Rica
| | - Priscila Chaverri
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, Maryland, USA
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San Jose, Costa Rica.
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica.
- Escuela de Química, Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica.
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25
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Arroyo J, Salazar-Sánchez L, Jiménez-Cruz G, Chaverri P, Arrieta-Bolaños E, Morera B. Prevalence and geographic distribution of haemophilia in Costa Rica. Hamostaseologie 2017. [DOI: 10.1055/s-0037-1619065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
SummaryHaemophilia is the most frequent hereditary haemorrhagic illness and it is due to the deficiency of coagulation factors VIII (haemophilia A, HA) or IX (haemophilia B, HB).The prevalence of this disease varies according to the country, those having better survival rates having also higher prevalences. Specifically in Costa Rica, there are around 130 HA and 30 HB families. This study reports the prevalence and a spatial distribution analysis of both types of the disease in this country. The prevalence of haemophilia in this country is 7 cases per 100 000 men, for HA it is 6 cases per 100 000 and for HB it is 1 case per 100 000 male inhabitants. The prevalence of this disease is low when compared with other populations. This low prevalence could be due to the many patients that have died because of infection with human immunodeficiency virus during the 1980s. The prevalence of haemophilia in Costa Rica is almost one half of that present in developed countries. Nevertheless, the ratio between HA and HB follows world tendency: 5 : 1. In this study, nationwide geographical distribution maps were drawn in order to visualize the origin of severe cases and how this influences the pattern of distribution for both types of haemophilia. By means of these maps, it was possible to state that there is no association between the sites of maximum prevalence of mutated alleles and ethnicity. With this study, haemophilia prevalence distribution maps can be used to improve efforts for the establishment of hemophilia clinics or specialized health centers in those areas which hold the highest prevalences in this country. Also, this knowledge can be applied to improve treatment skills and offer the possibility of developing focused genetic counseling for these populations.
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26
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González CD, Chaverri P. Corinectria, a new genus to accommodate Neonectria fuckeliana and C. constricta sp. nov. from Pinus radiata in Chile. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1343-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Affiliation(s)
- Priscila Chaverri
- Pennsylvania State University, Department of Plant Pathology, 301 Buckhout Laboratory, University Park, Pennsylvania 16802
| | - Lisa A. Castlebury
- U.S.D.A.-A.R.S., Systematic Botany and Mycology Laboratory, Room 304, B011A, 10300 Baltimore Avenue, Beltsville, Maryland 20705
| | - Barrie E. Overton
- Pennsylvania State University, Department of Plant Pathology, 301 Buckhout Laboratory, University Park, Pennsylvania 16802
| | - Gary J. Samuels
- U.S.D.A.-A.R.S., Systematic Botany and Mycology Laboratory, Room 304, B011A, 10300 Baltimore Avenue, Beltsville, Maryland 20705
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28
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Lu B, Druzhinina IS, Fallah P, Chaverri P, Gradinger C, Kubicek CP, Samuels GJ. Hypocrea/Trichodermaspecies with pachybasium-like conidiophores: teleomorphs forT. minutisporumandT. polysporumand their newly discovered relatives. Mycologia 2017. [DOI: 10.1080/15572536.2005.11832980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Bingsheng Lu
- Department of Plant Pathology, Agronomy College, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Irina S. Druzhinina
- Section of Applied Biochemistry and Gene Technology, Institute of Chemical Engineering, TU Wien, Getreidemarkt 9-166.5, A-1060 Wien, Austria
| | | | - Priscila Chaverri
- Pennsylvania State University, Department of Plant Pathology, 301 Buckhout Laboratory, University Park, Pennsylvania 16802
| | | | - Christian P. Kubicek
- Section of Applied Biochemistry and Gene Technology, Institute of Chemical Engineering, TU Wien, Getreidemarkt 9-166.5, A-1060 Wien, Austria
| | - Gary J. Samuels
- USDA-ARS, Systematic Botany and Mycology Laboratory, Room 304, B-011A, BARC-West, Beltsville, Maryland 20705-2350
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29
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Affiliation(s)
- Joseph F. Bischoff
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894
| | - Priscila Chaverri
- Systematic Botany and Mycology Laboratory, United States Department of Agriculture, Bethesda, Beltsville, Maryland 20705
| | - James F. White
- Department of Plant Biology and Pathology, Cook College, Rutgers University, New Brunswick, New Jersey 08901
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30
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Chaverri P, Bischoff JF, Evans HC, Hodge KT. Regiocrella, a new entomopathogenic genus with a pycnidial anamorph and its phylogenetic placement in the Clavicipitaceae. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832732] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Priscila Chaverri
- Department of Plant Pathology, Cornell University, 334 Plant Science Building, Ithaca, New York 14853
| | - Joseph F. Bischoff
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894
| | - Harry C. Evans
- CABI Bioscience UK Centre (Ascot), Silwood Park, Buckhurst Road, Ascot, BERKS. SL5 7TA, U. K
| | - Kathie T. Hodge
- Department of Plant Pathology, Cornell University, 334 Plant Science Building, Ithaca, New York 14853
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31
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Affiliation(s)
- Priscila Chaverri
- Department of Plant Pathology, Cornell University, 334 Plant Science Building, Ithaca, New York 14853
| | - Gary J. Samuels
- USDA-ARS, Systematic Botany and Mycology, Laboratory, Room 304, B-011A, 10300 Baltimore, Ave., Beltsville, Maryland 20705
| | - Kathie T. Hodge
- Department of Plant Pathology, Cornell University, 334 Plant Science Building, Ithaca, New York 14853
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32
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Rojas EI, Herre EA, Mejía LC, Arnold AE, Chaverri P, Samuels GJ. Endomelanconiopsis, a new anamorph genus in the Botryosphaeriaceae. Mycologia 2017; 100:760-75. [DOI: 10.3852/07-207] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Edward Allen Herre
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa, Ancon, Republic of Panama
| | - Luis C. Mejía
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, Foran Hall, New Brunswick, New Jersey 08901
| | - A. Elizabeth Arnold
- Division of Plant Pathology and Microbiology, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Priscila Chaverri
- Department of Biology, Howard University, 415 College Street NW, Washington D.C. 20059
| | - Gary J. Samuels
- United States Department of Agriculture, Agriculture Research Service, Systematic Mycology & Microbiology Laboratory, B-011A, Room 304, 10300 Baltimore Ave., Beltsville, Maryland 20705
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33
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Hirooka Y, Kobayashi T, Ono T, Rossman AY, Chaverri P. Verrucostoma, a new genus in the Bionectriaceae from the Bonin Islands, Japan. Mycologia 2017; 102:418-29. [DOI: 10.3852/09-137] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yuuri Hirooka
- United States Department of Agriculture, Agriculture Research Service, Systematic Mycology and Microbiology Laboratory, Beltsville, Maryland 20705
| | - Takao Kobayashi
- Department of International Agriculture Development, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Tsuyoshi Ono
- Tokyo Metropolitan Agricultural and Forestry Research Center, 3-8-1 Fujimi-cho, Tachikawa, Tokyo 190-0013, Japan
| | - Amy Y. Rossman
- United States Department of Agriculture, Agriculture Research Service, Systematic Mycology and Microbiology Laboratory, Beltsville, Maryland 20705
| | - Priscila Chaverri
- Department of Plant Sciences and Landscape Architecture, 2112 Plant Sciences Building, University of Maryland, College Park, Maryland 20742
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34
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Chaverri P, Gazis RO, Samuels GJ. Trichoderma amazonicum, a new endophytic species on Hevea brasiliensis and H. guianensis from the Amazon basin. Mycologia 2017; 103:139-51. [DOI: 10.3852/10-078] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Romina O. Gazis
- University of Maryland, Department of Plant Sciences and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland 20742
| | - Gary J. Samuels
- United States Department of Agriculture, Agriculture Research Service, Systematic Mycology and Microbiology Laboratory, Room 304, B-011A, 10300 Beltsville Avenue, Beltsville, Maryland 20705
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35
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Herrera CS, Rossman AY, Samuels GJ, Chaverri P. Pseudocosmospora, a new genus to accommodate Cosmospora vilior and related species. Mycologia 2017; 105:1287-305. [DOI: 10.3852/12-395] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Cesar S. Herrera
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland 20742
| | | | - Gary J. Samuels
- United States Department of Agriculture, Agriculture Research Service, Systematic Mycology and Microbiology Laboratory, B-010A, 10300 Beltsville, Maryland 20705
| | - Priscila Chaverri
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland 20742
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36
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Robbertse B, Strope PK, Chaverri P, Gazis R, Ciufo S, Domrachev M, Schoch CL. Improving taxonomic accuracy for fungi in public sequence databases: applying 'one name one species' in well-defined genera with Trichoderma/Hypocrea as a test case. Database (Oxford) 2017; 2017:4553317. [PMID: 29220466 PMCID: PMC5641268 DOI: 10.1093/database/bax072] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 01/18/2023]
Abstract
The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation effort together with numerous fungal taxonomy experts attempted to cover as many orders as possible, we extended our latest focus to the family and genus ranks. We focused on Trichoderma for several reasons, mainly because the asexual and sexual synonyms were well documented, and a list of proposed names and type material were recently proposed and published. In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database. A name status report is available here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi. As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species. Additionally, to aid in the cross referencing of data from single loci and genomes we have collected a list of quality records of the RPB2 gene obtained from type material in GenBank that could help validate future submissions. During the process of curation misidentified genomes were discovered, and sequence records from type material were found hidden under previous classifications. Source metadata curation, although more cumbersome, proved to be useful as confirmation of the type material designation. Database URL:http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353
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Affiliation(s)
- Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pooja K Strope
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Romina Gazis
- Department of Entomology & Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Stacy Ciufo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Domrachev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
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Rossman AY, Allen WC, Braun U, Castlebury LA, Chaverri P, Crous PW, Hawksworth DL, Hyde KD, Johnston P, Lombard L, Romberg M, Samson RA, Seifert KA, Stone JK, Udayanga D, White JF. Overlooked competing asexual and sexually typified generic names of Ascomycota with recommendations for their use or protection. IMA Fungus 2016; 7:289-308. [PMID: 27990336 PMCID: PMC5159600 DOI: 10.5598/imafungus.2016.07.02.09] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 11/15/2016] [Indexed: 11/10/2022] Open
Abstract
With the change to one scientific name for fungal species, numerous papers have been published with recommendations for use or protection of competing generic names in major groups of ascomycetes. Although genera in each group of fungi were carefully considered, some competing generic names were overlooked. This paper makes recommendations for additional competing genera not considered in previous papers. Chairs of relevant Working Groups of the ICTF were consulted in the development of these recommendations. A number of generic names need protection, specifically Amarenographium over Amarenomyces, Amniculicola over Anguillospora, Balansia over Ephelis, Claviceps over Sphacelia, Drepanopeziza over Gloeosporidiella and Gloeosporium, Golovinomyces over Euoidium, Holwaya over Crinium, Hypocrella over Aschersonia, Labridella over Griphosphaerioma, Metacapnodium over Antennularia, and Neonectria over Cylindrocarpon and Heliscus. The following new combinations are made: Amniculicola longissima, Atichia maunauluana, Diaporthe columnaris, D. liquidambaris, D. longiparaphysata, D. palmicola, D. tersa, Elsinoë bucidae, E.caricae, E. choisyae, E. paeoniae, E. psidii, E. zorniae, Eupelte shoemakeri, Godronia myrtilli, G. raduloides, Sarcinella mirabilis, S. pulchra, Schizothyrium jamaicense, and Trichothallus niger. Finally, one new species name, Diaporthe azadirachte, is introduced to validate an earlier name, and the conservation of Discula with a new type, D. destructiva, is recommended.
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Affiliation(s)
- Amy Y Rossman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - W Cavan Allen
- Systematic Mycology and Microbiology Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Uwe Braun
- Martin Luther University, Institute of Biology, Department of Geobotany and Botanical Garden, Herbarium, Neuwerk 21, 06099 Halle (Saale), Germany
| | - Lisa A Castlebury
- Systematic Mycology and Microbiology Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Escuela de Biología, Universidad de Costa Rica, San Pedro San José, Costa Rica
| | - Pedro W Crous
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands; Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - David L Hawksworth
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramón y Cajal s/n, Madrid 28040, Spain; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey TW9 3DS, UK
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Peter Johnston
- Landcare Research, Private Bag 92170, Auckland 1142, New Zealand
| | - Lorenzo Lombard
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - Megan Romberg
- USDA-APHIS National Identification Services, Beltsville, MD 20705, USA
| | - Rob A Samson
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - Keith A Seifert
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Jeffrey K Stone
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Dhanushka Udayanga
- Systematic Mycology and Microbiology Laboratory, USDA-ARS, Beltsville, MD 20705, USA
| | - James F White
- Department of Plant Biology & Pathology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ 08901, USA
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Salgado-Salazar C, Rossman AY, Chaverri P. The genus Thelonectria (Nectriaceae, Hypocreales, Ascomycota) and closely related species with cylindrocarpon-like asexual states. FUNGAL DIVERS 2016. [DOI: 10.1007/s13225-016-0365-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Montoya QV, Meirelles LA, Chaverri P, Rodrigues A. Unraveling Trichoderma species in the attine ant environment: description of three new taxa. Antonie Van Leeuwenhoek 2016; 109:633-51. [PMID: 26885975 DOI: 10.1007/s10482-016-0666-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 02/03/2016] [Indexed: 11/25/2022]
Abstract
Fungus-growing "attine" ants forage diverse substrates to grow fungi for food. In addition to the mutualistic fungal partner, the colonies of these insects harbor a rich microbiome composed of bacteria, filamentous fungi and yeasts. Previous work reported some Trichoderma species in the fungus gardens of leafcutter ants. However, no studies systematically addressed the putative association of Trichoderma with attine ants, especially in non-leafcutter ants. Here, a total of 62 strains of Trichoderma were analyzed using three molecular markers (ITS, tef1 and rpb2). In addition, 30 out of 62 strains were also morphologically examined. The strains studied correspond to the largest sampling carried out so far for Trichoderma in the attine ant environment. Our results revealed the richness of Trichoderma in this environment, since we found 20 Trichoderma species, including three new taxa described in the present work (Trichoderma attinorum, Trichoderma texanum and Trichoderma longifialidicum spp. nov.) as well as a new phylogenetic taxon (LESF 545). Moreover, we show that all 62 strains grouped within different clades across the Trichoderma phylogeny, which are identical or closely related to strains derived from several other environments. This evidence supports the transient nature of the genus Trichoderma in the attine ant colonies. The discovery of three new species suggests that the dynamic foraging behavior of these insects might be responsible for accumulation of transient fungi into their colonies, which might hold additional fungal taxa still unknown to science.
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Affiliation(s)
- Quimi Vidaurre Montoya
- Department of Biochemistry and Microbiology, UNESP - São Paulo State University, Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, CEP: 13.506-900, Brazil
| | - Lucas Andrade Meirelles
- Department of Biochemistry and Microbiology, UNESP - São Paulo State University, Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, CEP: 13.506-900, Brazil.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, 2112 Plant Sciences Building, College Park, MD, 20742, USA.,Escuela de Biología, Universidad de Costa Rica, Apartado 11501-2060, San Pedro, San José, Costa Rica
| | - Andre Rodrigues
- Department of Biochemistry and Microbiology, UNESP - São Paulo State University, Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, CEP: 13.506-900, Brazil.
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Herrera CS, Hirooka Y, Chaverri P. Pseudocospeciation of the mycoparasite Cosmospora with their fungal hosts. Ecol Evol 2016; 6:1504-14. [PMID: 27087926 PMCID: PMC4775519 DOI: 10.1002/ece3.1967] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/28/2015] [Accepted: 01/03/2016] [Indexed: 01/07/2023] Open
Abstract
Species of Cosmospora are parasites of other fungi (mycoparasites), including species belonging to the Xylariales. Based on prior taxonomic work, these fungi were determined to be highly host specific. We suspected that the association of Cosmospora and their hosts could not be a result of random chance, and tested the cospeciation of Cosmospora and the their hosts with contemporary methods (e.g., ParaFit, PACo, and Jane). The cophylogeny of Cosmospora and their hosts was found to be congruent, but only host‐parasite links in more recent evolutionary lineages of the host were determined as coevolutionary. Reconciliation reconstructions determined at least five host‐switch events early in the evolution of Cosmospora. Additionally, the rates of evolution between Cosmospora and their hosts were unequal. This pattern is more likely to be explained by pseudocospeciation (i.e., host switches followed by cospeciation), which also produces congruent cophylogenies.
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Affiliation(s)
- Cesar S Herrera
- Department of Plant Science and Landscape Architecture University of Maryland 2112 Plant Sciences Building College Park Maryland 20742 United States
| | - Yuuri Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience Hosei University 3-7-2 Kajino-cho Koganei Tokyo Japan
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture University of Maryland 2112 Plant Sciences Building College Park Maryland 20742 United States; Escuela de Biología Universidad de Costa Rica Apartado 11501-2060 San Pedro San José Costa Rica
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41
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Gazis R, Chaverri P. Wild trees in the Amazon basin harbor a great diversity of beneficial endosymbiotic fungi: is this evidence of protective mutualism? FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2015.04.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Chaverri P, Branco-Rocha F, Jaklitsch W, Gazis R, Degenkolb T, Samuels GJ. Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains. Mycologia 2015; 107:558-590. [PMID: 25661720 PMCID: PMC4885665 DOI: 10.3852/14-147] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 01/05/2015] [Indexed: 02/04/2023]
Abstract
Trichoderma harzianum is known as a cosmopolitan, ubiquitous species associated with a wide variety of substrates. It is possibly the most commonly used name in agricultural applications involving Trichoderma, including biological control of plant diseases. While various studies have suggested that T. harzianum is a species complex, only a few cryptic species are named. In the present study the taxonomy of the T. harzianum species complex is revised to include at least 14 species. Previously named species included in the complex are T. guizhouense, T. harzianum, and T. inhamatum. Two new combinations are proposed, T. lentiforme and T. lixii. Nine species are described as new, T. afarasin, T. afroharzianum, T. atrobrunneum, T. camerunense, T. endophyticum, T. neotropicale, T. pyramidale, T. rifaii and T. simmonsii. We isolated Trichoderma cultures from four commercial biocontrol products reported to contain T. harzianum. None of the biocontrol strains were identified as T. harzianum s. str. In addition, the widely applied culture 'T. harzianum T22' was determined to be T. afroharzianum. Some species in the T. harzianum complex appear to be exclusively endophytic, while others were only isolated from soil. Sexual states are rare. Descriptions and illustrations are provided. A secondary barcode, nuc translation elongation factor 1-α (TEF1) is needed to identify species in this complex.
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Affiliation(s)
- Priscila Chaverri
- University of Maryland, Department of Plant Science and Landscape
Architecture, 2112 Plant Sciences Building, College Park, Maryland 20742,
and Universidad de Costa Rica, Escuela de Biología, Apartado
11501-2060, San Pedro, San José, Costa Rica
| | - Fabiano Branco-Rocha
- Empresa de Pesquisa Agropecuária e Extensão Rural de
Santa Catarina - EPAGRI, Estação Experimental de São
Joaquim, São Joaquim, Santa Catarina, 88600-000, Brazil
| | - Walter Jaklitsch
- University of Vienna, Department of Systematic and Evolutionary
Botany, Faculty Centre of Biodiversity, Rennweg 14, 1030 Vienna,
Austria
| | - Romina Gazis
- Clark University, Biology Department, 950 Main Street, Worcester,
Massachusetts 01610
| | - Thomas Degenkolb
- Interdisciplinary Research Centre for BioSystems, Land Use and
Nutrition (IFZ), Department of Food Science, Institute of Nutritional
Science, University of Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen,
Germany
| | - Gary J. Samuels
- United States Dept. of Agriculture, Agriculture Research Service,
Systematic Mycology and Microbiology Lab., B-010, Beltsville, Maryland
20705
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Degenkolb T, Fog Nielsen K, Dieckmann R, Branco-Rocha F, Chaverri P, Samuels GJ, Thrane U, von Döhren H, Vilcinskas A, Brückner H. Peptaibol, Secondary-Metabolite, and Hydrophobin Pattern of Commercial Biocontrol Agents Formulated with Species of theTrichoderma harzianumComplex. Chem Biodivers 2015; 12:662-84. [DOI: 10.1002/cbdv.201400300] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Indexed: 11/05/2022]
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Herrera CS, Rossman AY, Samuels GJ, Pereira OL, Chaverri P. Systematics of the Cosmospora viliuscula species complex. Mycologia 2015; 107:532-57. [PMID: 25800252 DOI: 10.3852/14-122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 02/02/2015] [Indexed: 11/10/2022]
Abstract
The genus Cosmospora includes nectrioid fungi that grow on polypores and xylariaceous fungi. The collections growing on xylariaceous fungi have been identified recently as Cosmospora viliuscula. In this paper the phylogeny and taxonomy of C. viliuscula are investigated. A phylogeny was generated with maximum likelihood and Bayesian inference methods applied to a three-partition dataset (ITS, 28S, MCM7-RPB1-TUB2). Based on these results, we demonstrate that Cosmospora viliuscula represents a diverse species complex comprising more than 10 species. Seven new species are described, including three single-strain lineages, and the sexual states of C. arxii and C. khandalensis are described for the first time. The sexual states of these fungi tend to have a high degree of morphological homoplasy, making it difficult to differentiate among them based on morphological characters alone. However, the apparent host specificity of species in this complex aide in the diagnosis of these fungi. In addition, the RPB1 marker provides sufficient resolution to distinguish these fungi.
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Affiliation(s)
- Cesar S Herrera
- Department of Plant Science and Landscape Architecture, University of Maryland, 2112 Plant Sciences Building, College Park, Maryland 20742
| | - Amy Y Rossman
- Systematic Mycology and Microbiology Laboratory, USDA, B-010A, 10300 Baltimore Ave, Beltsville, Maryland 20705
| | - Gary J Samuels
- Systematic Mycology and Microbiology Laboratory, USDA, B-010A, 10300 Baltimore Ave, Beltsville, Maryland 20705
| | - Olinto Liparini Pereira
- Departamento de Fitopatologia, Universidade Federal de Viçosa, 36570-000 Viçosa, Minas Gerais, Brasil
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, 2112 Plant Sciences Building, College Park, Maryland 20742 and Escuela de Biología, Universidad de Costa Rica, Apartado 11501-2060, San 15 Pedro, San José, Costa Rica
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45
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Martin R, Gazis R, Skaltsas D, Chaverri P, Hibbett D. Unexpected diversity of basidiomycetous endophytes in sapwood and leaves of Hevea. Mycologia 2015; 107:284-97. [PMID: 25572095 DOI: 10.3852/14-206] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Research on fungal endophytes has expanded dramatically in recent years, but little is known about the diversity and ecological roles of endophytic basidiomycetes. Here we report the analysis of 310 basidiomycetous endophytes isolated from wild and planted populations of the rubber tree genus, Hevea. Species accumulation curves were nonasymptotic, as in the majority of endophyte surveys, indicating that more sampling is needed to recover the true diversity of the community. One hundred eighteen OTUs were delimited, representing nine orders of Basidiomycota (Agaricales, Atheliales, Auriculariales, Cantharellales, Hymenochaetales, Polyporales, Russulales, Septobasidiales, Tremellales). The diversity of basidiomycetous endophytes found inhabiting wild populations of Hevea was comparable to that present in plantations. However, when samples were segregated by tissue type, sapwood of wild populations was found to contain a higher number of species than sapwood of planted trees. Seventy-five percent of isolates were members of the Polyporales, the majority in the phlebioid clade. Most of the species belong to clades known to cause a white-rot type of wood decay. Two species in the insect-associated genus Septobasidium were isolated. The most frequently isolated genera included Bjerkandera, Ceriporia, Phanerochaete, Phlebia, Rigidoporus, Tinctoporellus, Trametes (Polyporales), Peniophora, Stereum (Russulales) and Coprinellus (Agaricales), all of which have been reported as endophytes from a variety of hosts, across wide geographic locations. Literature records on the geographic distribution and host association of these genera revealed that their distribution and substrate affinity could be extended if the endophytic niche was investigated as part of fungal biodiversity surveys.
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Affiliation(s)
- Rachael Martin
- Clark University, Biology Department, 950 Main Street, Worcester, Massachusetts 01610
| | - Romina Gazis
- Clark University, Biology Department, 950 Main Street, Worcester, Massachusetts 01610
| | - Demetra Skaltsas
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland 20742
| | - Priscila Chaverri
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland 20742, and Universidad de Costa Rica, Escuela de Biología, Apdo. 11501-2060, San Pedro, San José, Costa Rica
| | - David Hibbett
- Clark University, Biology Department, 950 Main Street, Worcester, Massachusetts 01610
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Gazis R, Skaltsas D, Chaverri P. Novel endophytic lineages of Tolypocladium provide new insights into the ecology and evolution of Cordyceps-like fungi. Mycologia 2014; 106:1090-105. [PMID: 24987126 DOI: 10.3852/13-346] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The objective of this study was to identify a group of unknown endophytic fungal isolates from the living sapwood of wild and planted Hevea (rubber tree) populations. Three novel lineages of Tolypocladium are described based on molecular and morphological data. Findings from this study open a window for novel hypotheses regarding the ecology and role of endophytes within plant communities as well as trait evolution and potential forces driving diversification of Cordyceps-like fungi. This study stresses the importance of integrating asexual and sexual fungal states for a more complete understanding of the natural history of this diverse group. In addition, it highlights the study of fungi in the sapwood of tropical trees as habitat for the discovery of novel fungal lineages and substrate associations.
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Affiliation(s)
- Romina Gazis
- Clark University, Biology Department, 950 Main Street, Worcester, Massachusetts 01610
| | - Demetra Skaltsas
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland 20742
| | - Priscila Chaverri
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland 20742, and Universidad de Costa Rica, Escuela de Biología, Apdo. 11501-2060, San Pedro, San José, Costa Rica
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Salgado-Salazar C, Rossman AY, Samuels GJ, Hirooka Y, Sanchez RM, Chaverri P. Phylogeny and taxonomic revision of Thelonectria discophora (Ascomycota, Hypocreales, Nectriaceae) species complex. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0280-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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48
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Salgado-Salazar C, Rossman AY, Chaverri P. Not as ubiquitous as we thought: taxonomic crypsis, hidden diversity and cryptic speciation in the cosmopolitan fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota). PLoS One 2013; 8:e76737. [PMID: 24204665 PMCID: PMC3799981 DOI: 10.1371/journal.pone.0076737] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 08/29/2013] [Indexed: 11/29/2022] Open
Abstract
The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan species or an assemblage of sibling species, we conducted various phylogenetic analyses, including standard gene concatenation, Bayesian concordance methods, and coalescent-based species tree reconstruction on isolates collected from a wide geographic range. Results show that diversity among isolates referred as T. discophora is greatly underestimated and that it represents a species complex. Within this complex, sixteen distinct highly supported lineages were recovered, each of which has a restricted geographic distribution and ecology. The taxonomic status of isolates regarded as T. discophora is reconsidered, and the assumed cosmopolitan distribution of this species is rejected. We discuss how assumptions about geographically widespread species have implications regarding their taxonomy, true diversity, biological diversity conservation, and ecological functions.
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Affiliation(s)
- Catalina Salgado-Salazar
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, United States of America
| | - Amy Y. Rossman
- Systematic Mycology and Microbiology Laboratory, Agriculture Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, United States of America
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Chaverri P, Samuels GJ. Evolution of habitat preference and nutrition mode in a cosmopolitan fungal genus with evidence of interkingdom host jumps and major shifts in ecology. Evolution 2013; 67:2823-37. [PMID: 24094336 DOI: 10.1111/evo.12169] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 05/14/2013] [Indexed: 01/11/2023]
Abstract
Host jumps by microbial symbionts are often associated with bursts of species diversification driven by the exploitation of new adaptive zones. The objective of this study was to infer the evolution of habitat preference (decaying plants, soil, living fungi, and living plants), and nutrition mode (saprotrophy and mycoparasitism) in the fungal genus Trichoderma to elucidate possible interkingdom host jumps and shifts in ecology. Host and ecological role shifts were inferred by phylogenetic analyses and ancestral character reconstructions. The results support several interkingdom host jumps and also show that the preference for a particular habitat was gained or lost multiple times. Diversification analysis revealed that mycoparasitism is associated with accelerated speciation rates, which then suggests that this trait may be linked to the high number of species in Trichoderma. In this study it was also possible to infer the cryptic roles that endophytes or soil inhabitants play in their hosts by evaluating their closest relatives and determining their most recent ancestors. Findings from this study may have implications for understanding certain evolutionary processes such as species radiations in some hyperdiverse groups of fungi, and for more applied fields such as the discovery and development of novel biological control strategies.
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Affiliation(s)
- Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, 2112 Plant Science Building, College Park, Maryland, 20742.
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50
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Rossman AY, Seifert KA, Samuels GJ, Minnis AM, Schroers HJ, Lombard L, Crous PW, Põldmaa K, Cannon PF, Summerbell RC, Geiser DM, Zhuang WY, Hirooka Y, Herrera C, Salgado-Salazar C, Chaverri P. Genera in Bionectriaceae, Hypocreaceae, and Nectriaceae (Hypocreales) proposed for acceptance or rejection. IMA Fungus 2013; 4:41-51. [PMID: 23898411 PMCID: PMC3719205 DOI: 10.5598/imafungus.2013.04.01.05] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 03/23/2013] [Indexed: 11/24/2022] Open
Abstract
With the recent changes concerning pleomorphic fungi in the new InternationalCode of Nomenclature for algae, fungi, and plants (ICN), it is necessary to propose the acceptance or protection of sexual morph-typified or asexual morph-typified generic names that do not have priority, or to propose the rejection or suppression1 of competing names. In addition, sexual morph-typified generic names, where widely used, must be proposed for rejection or suppression in favour of asexual morph-typified names that have priority, or the latter must be proposed for conservation or protection. Some pragmatic criteria used for deciding the acceptance or rejection of generic names include: the number of name changes required when one generic name is used over another, the clarity of the generic concept, their relative frequencies of use in the scientific literature, and a vote of interested mycologists. Here, twelve widely used generic names in three families of Hypocreales are proposed for acceptance, either by conservation or protection, despite their lack of priority of publication, or because they are widely used asexual morph-typified names. Each pair of generic names is evaluated, with a recommendation as to the generic name to be used, and safeguarded, either through conservation or protection. Four generic names typified by a species with a sexual morph as type that are younger than competing generic names typified by a species with an asexual morph type, are proposed for use. Eight older generic names typified by species with an asexual morph as type are proposed for use over younger competing generic names typified by a species with a sexual morph as type. Within Bionectriaceae,Clonostachys is recommended over Bionectria; in Hypocreaceae,Hypomyces is recommended over Cladobotryum, Sphaerostilbella over Gliocladium, and Trichoderma over Hypocrea; and in Nectriaceae,Actinostilbe is recommended over Lanatonectria, Cylindrocladiella over Nectricladiella, Fusarium over Gibberella, Gliocephalotrichum over Leuconectria, Gliocladiopsis over Glionectria, Nalanthamala over Rubrinectria, Nectria over Tubercularia, and Neonectria over Cylindrocarpon.
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Affiliation(s)
- Amy Y Rossman
- Systematic Mycology & Microbiology Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA
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