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Steenwyk JL, Balamurugan C, Raja HA, Gonçalves C, Li N, Martin F, Berman J, Oberlies NH, Gibbons JG, Goldman GH, Geiser DM, Houbraken J, Hibbett DS, Rokas A. Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus. Microbiol Spectr 2024; 12:e0398023. [PMID: 38445873 PMCID: PMC10986620 DOI: 10.1128/spectrum.03980-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/18/2024] [Indexed: 03/07/2024] Open
Abstract
Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus Aspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly available Aspergillus genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.
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Affiliation(s)
- Jacob L. Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Charu Balamurugan
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Carla Gonçalves
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Ningxiao Li
- Department of Plant Pathology, University of California, Davis, California, USA
- USDA-ARS, Salinas, California, USA
| | | | - Judith Berman
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Gustavo H. Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - David M. Geiser
- Department of Plant Pathology and Environmental Microbiology, Penn State University, University Park, Pennsylvania, USA
| | - Jos Houbraken
- Food and Indoor Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - David S. Hibbett
- Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg, Heidelberg, Germany
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2
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Cazabonne J, Walker AK, Lesven J, Haelewaters D. Singleton-based species names and fungal rarity: Does the number really matter? IMA Fungus 2024; 15:7. [PMID: 38504339 PMCID: PMC10953280 DOI: 10.1186/s43008-023-00137-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/13/2023] [Indexed: 03/21/2024] Open
Abstract
Fungi are among the least known organisms on earth, with an estimated number of species between 1.5 and 10 million. This number is expected to be refined, especially with increasing knowledge about microfungi in undersampled habitats and increasing amounts of data derived from environmental DNA sequencing. A significant proportion of newly generated sequences fail to match with already named species, and thus represent what has been referred to as fungal "dark taxa". Due to the challenges associated with observing, identifying, and preserving sporophores, many macro- and microfungal species are only known from a single collection, specimen, isolate, and/or sequence-a singleton. Mycologists are consequently used to working with "rare" sequences and specimens. However, rarity and singleton phenomena lack consideration and valorization in fungal studies. In particular, the practice of publishing new fungal species names based on a single specimen remains a cause of debate. Here, we provide some elements of reflection on this issue in the light of the specificities of the fungal kingdom and global change context. If multiple independent sources of data support the existence of a new taxon, we encourage mycologists to proceed with formal description, irrespective of the number of specimens at hand. Although the description of singleton-based species may not be considered best practice, it does represent responsible science in the light of closing the Linnean biodiversity shortfall.
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Affiliation(s)
- Jonathan Cazabonne
- Ecology Research Group of Abitibi RCM, Forest Research Institute, Université du Québec en Abitibi-Témiscamingue, Amos, QC, J9T 2L8, Canada.
- Centre for Forest Research, Université du Québec à Montréal, Montreal, QC, H3C 3P8, Canada.
| | - Allison K Walker
- Department of Biology, Acadia University, Wolfville, NS, B4P 2R6, Canada
| | - Jonathan Lesven
- Laboratoire Chrono-Environnement, UMR 6249 CNRS, Université de Bourgogne Franche-Comté, 25000, Besançon, France
- Forest Research Institute, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, J9X 5E4, Canada
| | - Danny Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, 9000, Ghent, Belgium.
- Faculty of Science, University of South Bohemia, 370 05, Ceske Budejovice, Czech Republic.
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, 80309, USA.
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic.
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3
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Kandemir H, Decock C, Hernández-Restrepo M, Labuda R, Houbraken J, Ilkit M, de Hoog GS. 200 years of taxonomic confusion: Sporendonema and allies. Antonie Van Leeuwenhoek 2024; 117:53. [PMID: 38483617 PMCID: PMC10940481 DOI: 10.1007/s10482-024-01935-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/28/2024] [Indexed: 03/17/2024]
Abstract
The genus Sporendonema (Gymnoascaceae, Onygenales) was introduced in 1827 with the type species S. casei for a red mould on cheese. Cheese is a consistent niche for this species. Sphaerosporium equinum is another species classified in Gymnoascaceae and has also been reported from cheese. Recently, other habitats have been reported for both Sporendonema casei and Sphaerosporium equinum. The present study aimed to investigate the taxonomy of Sporendonema and Sphaerosporium, as well as a close neighbour, Arachniotus. Two strains of Hormiscium aurantiacum, another related cheese-associated species were also included in the analyses. Strains were evaluated in terms of macro- and micromorphology, physiology including salt tolerance, growth rate at different temperatures, casein degradation, cellulase activity, lipolytic activity, and multi-locus phylogeny with sequences of the nuclear ribosomal internal transcribed spacer region, the D1-D2 region of the large subunit and partial β-tubulin locus sequences. The results showed that the analysed species were congeneric, and the generic names Arachniotus and Sphaerosporium should be reduced to the synonymy of Sporendonema. Therefore, four new combinations as well as one lectotype and one epitype were designated in Sporendonema. Two strains attributed to Sphaerosporium equinum from substrates other than cheese were found to be phylogenetically and morphologically deviant and were introduced as a new species named Sporendonema isthmoides.
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Affiliation(s)
- Hazal Kandemir
- Center of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Cony Decock
- Mycothéque de l'Université Catholique de Louvain, Earth and Life Institute, Louvain-La-Neuve, Belgium
| | | | - Roman Labuda
- Research Platform Bioactive Microbial Metabolites, Tulln/Donau, Austria
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Macit Ilkit
- Division of Medical Mycology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - G Sybren de Hoog
- Center of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
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4
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Braconcini M, Gorrasi S, Fenice M, Barghini P, Pasqualetti M. Rambellisea gigliensis and Rambellisea halocynthiae, gen. et spp. nov. (Lulworthiaceae) from the Marine Tunicate Halocynthia papillosa. J Fungi (Basel) 2024; 10:127. [PMID: 38392799 PMCID: PMC10890369 DOI: 10.3390/jof10020127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/24/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
In this study, 15 Lulworthiales strains isolated from the marine tunicate Halocynthia papillosa collected in the central Tyrrhenian Sea were characterized using a polyphasic approach (morpho-physiological, molecular, and phylogenetic analyses). Based on multi-locus phylogenetic inference and morphological characters, a new genus, Rambellisea, and two new species, R. halocynthiae and R. gigliensis (Lulworthiales), were proposed. Multi-locus phylogenetic analyses using the nuclear ribosomal regions of DNA (nrITS1-nr5.8S-nrITS2, nrLSU, and nrSSU) sequence data strongly supported the new taxa. Phylogenetic inference, estimated using Maximum Likelihood and Bayesian Inference, clearly indicates that Rambellisea gen. nov. forms a distinct clade within the order Lulworthiales. Moreover, the two new species were separated into distinct subclades, solidly supported by the analyses. This is the first report of Lulworthiales species isolated from animals.
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Affiliation(s)
- Martina Braconcini
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy
| | - Susanna Gorrasi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy
| | - Massimiliano Fenice
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy
- Laboratory of Applied Marine Microbiology, CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
| | - Paolo Barghini
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy
| | - Marcella Pasqualetti
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy
- Laboratory of Ecology of Marine Fungi, CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
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5
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Cabral TS, da Silva BDB, Vargas-Isla R, de Oliveira JJS, Ferreira JADS, Castro L, Martín MP, Ishikawa NK. Diversity of Neotropical stalked-puffball: Two new species of Tulostoma with reticulated spores. PLoS One 2023; 18:e0294672. [PMID: 38091271 PMCID: PMC10718411 DOI: 10.1371/journal.pone.0294672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
Species of the genus Tulostoma are easily recognizable by the presence of a spore sac, with a mouth from which spores are released, attached to a stipe. Tulostoma is a species-diverse genus with a worldwide distribution, and some attempts were made to delimitate species and to evaluate reliable taxonomic-informative characteristics for species identification. However, there is a notable information gap regarding Neotropical species, especially for geographic distribution and DNA data, which hampers further understanding of the infrageneric diversity, evolution, and ecology of this genus. Based on morphological analysis, molecular phylogenetics and geographic distribution, we propose here two new species of Tulostoma with reticulated spores, from the two threatened Brazilian geographical areas, Atlantic Forest and "campos rupestres" (rupestrian grassland), as well as we provide notes on the taxonomic rank of Tulostoma exasperatum var. ridleyi.
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Affiliation(s)
- Tiara Sousa Cabral
- Departamento de Parasitologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | | | - Ruby Vargas-Isla
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Jadson José Souza de Oliveira
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
- Programa de Pós-graduação em Botânica, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | | | - Laís Castro
- Fazenda Bananal, Paraty, Rio de Janeiro, Brazil
| | - María Paz Martín
- Departamento de Micología, Real Jardín Botánico-CSIC, Madrid, Spain
| | - Noemia Kazue Ishikawa
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
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6
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Liu XY, Liu SL, Wei HW, Wang XW, Yu J, Shen S, Zhou LW. Preliminary species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi in the Dabie Mountains, Central China reveal unexpected richness. IMA Fungus 2023; 14:23. [PMID: 37964331 PMCID: PMC10644440 DOI: 10.1186/s43008-023-00130-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/05/2023] [Indexed: 11/16/2023] Open
Abstract
Wood-inhabiting fungi have important economic values as well as playing a major ecological role in forest ecosystem cycles. The Dabie Mountains, at the junction of Henan, Hubei, and Anhui Provinces, Central China, provide an ideal climate and favorable niches for the speciation and diversification of various forms of life including fungi. We studied the species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi that revealed 175 wood-inhabiting basidiomycetous species, of which 20 represented unidentified species, based on morphological and phylogenetic analyses of 575 specimens collected from ten sampling sites. These species belonged to two classes, 11 orders, 42 families, and 106 genera of Basidiomycota, and included 12 edible species, 28 medicinal species, four poisonous species, and seven forest pathogens. Four types of fungal distribution pattern at the genus level were recognized for 65 genera, while another 41 genera could not be placed in any known distribution pattern. The five sampling sites in the eastern part of the Dabie Mountains had significantly higher species diversity and phylogenetic diversity of wood-inhabiting basidiomycetous fungi than those in the western part, and thus deserve priority in terms of conservation. The community of wood-inhabiting basidiomycetous fungi in the Dabie Mountains is generally affected by a combination of habitat filtering and competitive exclusion. This study provides a basis on which to build actions for the comprehensive recognition, utilization, and conservation of wood-inhabiting basidiomycetous fungi in the region.
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Affiliation(s)
- Xiang-Yang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Shi-Liang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Hao-Wen Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Xue-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jia Yu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Shan Shen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- College of Life Science, Liaoning University, Shenyang, 110036, People's Republic of China.
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7
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Schellenberger Costa D, Boehnisch G, Freiberg M, Govaerts R, Grenié M, Hassler M, Kattge J, Muellner-Riehl AN, Rojas Andrés BM, Winter M, Watson M, Zizka A, Wirth C. The big four of plant taxonomy - a comparison of global checklists of vascular plant names. THE NEW PHYTOLOGIST 2023; 240:1687-1702. [PMID: 37243532 DOI: 10.1111/nph.18961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/12/2023] [Indexed: 05/29/2023]
Abstract
Taxonomic checklists used to verify published plant names and identify synonyms are a cornerstone of biological research. Four global authoritative checklists for vascular plants exist: Leipzig Catalogue of Vascular Plants, World Checklist of Vascular Plants, World Flora Online (successor of The Plant List, TPL), and WorldPlants. We compared these four checklists in terms of size and differences across taxa. We matched taxon names of these checklists and TPL against each other, identified differences across checklists, and evaluated the consistency of accepted names linked to individual taxon names. We assessed geographic and phylogenetic patterns of variance. All checklists differed strongly compared with TPL and provided identical information on c. 60% of plant names. Geographically, differences in checklists increased from low to high latitudes. Phylogenetically, we detected strong variability across families. A comparison of name-matching performance on taxon names submitted to the functional trait database TRY, and a check of completeness of accepted names evaluated against an independent, expert-curated checklist of the family Meliaceae, showed a similar performance across checklists. This study raises awareness on the differences in data and approach across these checklists potentially impacting analyses. We propose ideas on the way forward exploring synergies and harmonizing the four global checklists.
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Affiliation(s)
- David Schellenberger Costa
- Department of Special Botany and Functional Biodiversity, Faculty of Life Sciences, University of Leipzig, Johannisallee 21-23, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr 4, 04103, Leipzig, Germany
| | - Gerhard Boehnisch
- Research Group Functional Biogeography, Max Planck Institute for Biogeochemistry, Hans-Knoell-Str. 10, 07745, Jena, Germany
| | - Martin Freiberg
- Department of Special Botany and Functional Biodiversity, Faculty of Life Sciences, University of Leipzig, Johannisallee 21-23, 04103, Leipzig, Germany
| | - Rafaël Govaerts
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Kew Road, Richmond, TW9 3DS, UK
| | - Matthias Grenié
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr 4, 04103, Leipzig, Germany
| | | | - Jens Kattge
- Research Group Functional Biogeography, Max Planck Institute for Biogeochemistry, Hans-Knoell-Str. 10, 07745, Jena, Germany
| | - Alexandra N Muellner-Riehl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr 4, 04103, Leipzig, Germany
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Faculty of Life Sciences, University of Leipzig, Johannisallee 21-23, 04103, Leipzig, Germany
| | - Blanca M Rojas Andrés
- Departamento de Botánica y Fisiología Vegetal, Universidad de Salamanca, Ave Licenciado Méndez Nieto s/n, 37007, Salamanca, Spain
- Biobanco de ADN Vegetal, Edificio Multiusos I+D+i, Universidad de Salamanca, Calle Espejo s/n, 37007, Salamanca, Spain
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr 4, 04103, Leipzig, Germany
| | - Mark Watson
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Alexander Zizka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr 4, 04103, Leipzig, Germany
- Department of Biology, Philipps-University Marburg, 35043, Marburg, Germany
| | - Christian Wirth
- Department of Special Botany and Functional Biodiversity, Faculty of Life Sciences, University of Leipzig, Johannisallee 21-23, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr 4, 04103, Leipzig, Germany
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8
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Deutsch KR, Graham JR, Boncristiani HF, Bustamante T, Mortensen AN, Schmehl DR, Wedde AE, Lopez DL, Evans JD, Ellis JD. Widespread distribution of honey bee-associated pathogens in native bees and wasps: Trends in pathogen prevalence and co-occurrence. J Invertebr Pathol 2023; 200:107973. [PMID: 37479057 DOI: 10.1016/j.jip.2023.107973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023]
Abstract
Pollinators have experienced significant declines in the past decade, in part due to emerging infectious diseases. Historically, studies have primarily focused on pathogens in the Western honey bee, Apis mellifera. However, recent work has demonstrated that these pathogens are shared by other pollinators and can negatively affect their health. Here, we surveyed honey bees and 15 native bee and wasp species for 13 pathogens traditionally associated with honey bees. The native bee and wasp species included 11 species not previously screened for pathogens. We found at least one honey bee-associated pathogen in 53% of native bee and wasp samples. The most widely distributed and commonly detected pathogens were the microsporidian Nosema ceranae, the bacterium Melissococcus plutonius, and the viruses deformed wing virus and black queen cell virus. The prevalence of viruses was generally higher in honey bees than in native bees and wasps. However, the prevalence of M. plutonius and the brood fungus Ascosphaera apis was significantly higher in some native bee species than in honey bees. The data also reveal novel trends in the association between co-occurring pathogens in honey bees and native bees and wasps at the pathogen community level. These results can inform the assessment of risks that native pollinator species face from pathogen stress, and indicate that many non-viral pathogens, notably M. plutonius and N. ceranae, are far more widely distributed and commonly found in native bees and wasps than previously thought.
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Affiliation(s)
| | - Jason R Graham
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA; Planet Bee Foundation, San Francisco, CA 94132, USA
| | - Humberto F Boncristiani
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA; Inside The Hive Media, Consulting Inc., Odenton, MD 21113, USA
| | - Tomas Bustamante
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA; Independent Collaborator, Dallas, TX, USA
| | - Ashley N Mortensen
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA; The New Zealand Institute for Plant and Food Research Limited, Bisley Road, Hamilton 3214, New Zealand
| | - Daniel R Schmehl
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA; Bayer CropScience LP, 700 Chesterfield Pwky. W., Chesterfield, MO 63017, USA
| | - Ashlyn E Wedde
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA; Driscoll's Global R&D, Watsonville, CA, USA
| | - Dawn L Lopez
- Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Jay D Evans
- Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - James D Ellis
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
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9
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Lopes RB, de Souza DA, Inglis PW, Faria M. Diversity of anamorphic Cordyceps (formerly Isaria) isolated from Brazilian agricultural sites. J Invertebr Pathol 2023; 200:107956. [PMID: 37356705 DOI: 10.1016/j.jip.2023.107956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 06/27/2023]
Abstract
A total of 53 anamorphic strains of Brazilian Cordyceps species currently maintained in a government-owned culture collection, were reassessed for diversity and species identity using multi-loci-based phylogenetic methods. The strains used in this study were originally obtained from soil samples or were isolated from insects of the orders Hemiptera, Lepidoptera, Coleoptera and Diptera, mostly from agricultural sites. A Bayesian phylogenetic tree was constructed based on a concatenation of five loci (ITS, LSU, RPB1, RPB2 and TEF). In a few cases of ambiguity, morphological traits were also considered for species delimitations. Considerable variability within the set of strains was detected and six Cordyceps species were identified: C. amoenerosea, C. fumosorosea, C. javanica, C. tenuipes and, for the first time, C. brevistroma and C. spegazzinii are reported in Brazil. Four other taxonomically equivocal groups, closely related to other known taxa (C. amoenerosea, C. cateniannulata, C. polyarthra and C. spegazzinii), were also recognized, although further studies will be required to confirm their identifications or their descriptions as new species. Cordyceps javanica was the most common species in our dataset, originally isolated from soil and several different insect orders, and includes 17 strains from the whitefly, Bemisia tabaci. Interestingly, strains previously identified as C. fumosorosea based on morphology and growth characteristics, were shown to be C. javanica, including the active ingredients of some commercial mycoinsecticides. Cordyceps farinosa, usually mentioned in the literature as occurring in Brazil, was not found in our study. Since most strains were from insect crop pests, further studies with hosts from non-agricultural settings or from environmental samples would be advisable for a deeper understanding of the occurrence of anamorphic Cordyceps in Brazil.
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Affiliation(s)
| | | | - Peter W Inglis
- Embrapa Genetic Resources and Biotechnology, Brasília, Federal District 70770-917, Brazil.
| | - Marcos Faria
- Embrapa Genetic Resources and Biotechnology, Brasília, Federal District 70770-917, Brazil.
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Bradshaw MJ, Aime MC, Rokas A, Maust A, Moparthi S, Jellings K, Pane AM, Hendricks D, Pandey B, Li Y, Pfister DH. Extensive intragenomic variation in the internal transcribed spacer region of fungi. iScience 2023; 26:107317. [PMID: 37529098 PMCID: PMC10387565 DOI: 10.1016/j.isci.2023.107317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/08/2023] [Accepted: 07/04/2023] [Indexed: 08/03/2023] Open
Abstract
Fungi are among the most biodiverse organisms in the world. Accurate species identification is imperative for studies on fungal ecology and evolution. The internal transcribed spacer (ITS) rDNA region has been widely accepted as the universal barcode for fungi. However, several recent studies have uncovered intragenomic sequence variation within the ITS in multiple fungal species. Here, we mined the genome of 2414 fungal species to determine the prevalence of intragenomic variation and found that the genomes of 641 species, about one-quarter of the 2414 species examined, contained multiple ITS copies. Of those 641 species, 419 (∼65%) contained variation among copies revealing that intragenomic variation is common in fungi. We proceeded to show how these copies could result in the erroneous description of hundreds of fungal species and skew studies evaluating environmental DNA (eDNA) especially when making diversity estimates. Additionally, many genomes were found to be contaminated, especially those of unculturable fungi.
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Affiliation(s)
- Michael J. Bradshaw
- Harvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Autumn Maust
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USA
| | - Swarnalatha Moparthi
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Keila Jellings
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Alexander M. Pane
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USA
| | - Dylan Hendricks
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USA
| | - Binod Pandey
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, USA
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Donald H. Pfister
- Harvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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11
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Balocchi F, Barnes I, Wingfield MJ, Ahumada R, Visagie CM. New Resinogalea species from Araucaria araucana resin in Chile and reclassification of the genus in the Cryptocaliciomycetidae. IMA Fungus 2023; 14:16. [PMID: 37596646 PMCID: PMC10439659 DOI: 10.1186/s43008-023-00122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023] Open
Abstract
Araucaria araucana is an ancient conifer, native to the mountain ranges in Chile and Argentina. These trees host a large number of organisms, mainly insects, strongly or even exclusively associated with them. The recent emergence of a novel canker disease on A. araucana has emphasised the importance of fungi associated with these iconic trees and has resulted in the discovery of various new species. In this study, we considered the identity of an unknown calicioid fungus consistently found on resin on the branches of A. araucana. Preliminary phylogenetic analyses placed isolates in the recently described sub-class Cryptocaliciomycetidae, closest to Cryptocalicium blascoi. However, the morphology of the ascomata and its occurrence in a unique niche suggested that the closest relative could be Resinogalea humboldtensis (Bruceomycetaceae, incertae sedis), a fungus with similar sporing structures found on resin of Araucaria humboldtensis in New Caledonia. There are no living cultures or sequence data available for either R. humboldtensis or its supposed closest relative, Bruceomyces castoris, precluding sequence-based comparisons. Morphological comparisons of the sporing structures on A. araucana confirmed that the ascomatal morphology of our unknown calicioid fungus and R. humboldtensis are almost identical and resemble each other more so than B. castoris or Cr. blascoi. A phylogenetic analysis based on the small subunit (SSU), internal transcribed spacer (ITS) and large subunit (LSU) rDNA regions resolved our strains into two clades with Cr. blascoi as its closest relative. Further analyses applying the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) based on ITS, mini chromosome maintenance protein complex (MCM7), RNA polymerase II second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF) gene regions, confirmed that strains represent two new species. Based on our morphological observations and phylogenetic analyses, we introduce two new Resinogalea species, R. araucana and R. tapulicola, and reclassify the genus in the subclass Cryptocaliciomycetidae.
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Affiliation(s)
- Felipe Balocchi
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, FABI, University of Pretoria, Pretoria, 0002, South Africa.
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, FABI, University of Pretoria, Pretoria, 0002, South Africa
| | - Rodrigo Ahumada
- Silviculture and Forest Health Division, Bioforest, Concepción, Chile
| | - Cobus M Visagie
- Department of Biochemistry, Genetics and Microbiology, FABI, University of Pretoria, Pretoria, 0002, South Africa
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Martinez A, Calhoun AC, Sadd BM. Investigating the influence of diet diversity on infection outcomes in a bumble bee ( Bombus impatiens) and microsporidian ( Nosema bombi) host-pathogen system. FRONTIERS IN INSECT SCIENCE 2023; 3:1207058. [PMID: 38469464 PMCID: PMC10926413 DOI: 10.3389/finsc.2023.1207058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/01/2023] [Indexed: 03/13/2024]
Abstract
Diet can have an array of both direct and indirect effects on an organism's health and fitness, which can influence the outcomes of host-pathogen interactions. Land use changes, which could impact diet quantity and quality, have imposed foraging stress on important natural and agricultural pollinators. Diet related stress could exacerbate existing negative impacts of pathogen infection. Accounting for most of its nutritional intake in terms of protein and many micronutrients, pollen can influence bee health through changes in immunity, infection, and various aspects of individual and colony fitness. We investigate how adult pollen consumption, pollen type, and pollen diversity influence bumble bee Bombus impatiens survival and infection outcomes for a microsporidian pathogen Nosema (Vairimorpha) bombi. Experimental pathogen exposures of larvae occurred in microcolonies and newly emerged adult workers were given one of three predominantly monofloral, polyfloral, or no pollen diets. Workers were assessed for size, pollen consumption, infection 8-days following adult-eclosion, survival, and the presence of extracellular microsporidian spores at death. Pollen diet treatment, specifically absence of pollen, and infection independently reduced survival, but we saw no effects of pollen, pollen type, or pollen diet diversity on infection outcomes. The latter suggests infection outcomes were likely already set, prior to differential diets. Although infection outcomes were not altered by pollen diet in our study, it highlights both pathogen infection and pollen availability as important for bumble bee health, and these factors may interact at different stages of bumble bee development, at the colony level, or under different dietary regimes.
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Affiliation(s)
| | | | - Ben M. Sadd
- School of Biological Sciences, Illinois State University, Normal, IL, United States
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13
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Rheindt FE, Bouchard P, Pyle RL, Welter-Schultes F, Aescht E, Ahyong ST, Ballerio A, Bourgoin T, Ceríaco LMP, Dmitriev D, Evenhuis N, Grygier MJ, Harvey MS, Kottelat M, Kluge N, Krell FT, Kojima JI, Kullander SO, Lucinda P, Lyal CHC, Scioscia CL, Whitmore D, Yanega D, Zhang ZQ, Zhou HZ, Pape T. Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice. PLoS Biol 2023; 21:e3002251. [PMID: 37607211 PMCID: PMC10443861 DOI: 10.1371/journal.pbio.3002251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023] Open
Abstract
Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of "species diagnosis" in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation of new editions of the International Code of Zoological Nomenclature and other Codes of bionomenclature.
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Affiliation(s)
- Frank E. Rheindt
- National University of Singapore, Department of Biological Sciences, Singapore
| | - Patrice Bouchard
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Richard L. Pyle
- Department of Natural Sciences, Bernice Pauahi Bishop Museum, Honolulu, Hawaii, United States of America
| | - Francisco Welter-Schultes
- Abteilung Evolution und Biodiversität der Tiere und Zoologisches Museum, Universität Göttingen, Göttingen, Germany
| | - Erna Aescht
- Biology Centre of the Upper Austrian Museum, Linz, Austria
| | - Shane T. Ahyong
- Australian Museum, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | | | - Thierry Bourgoin
- Institut Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-Sorbonne Université-EPHE- Université des Antilles, Museum National d’Histoire Naturelle, Paris, France
| | - Luis M. P. Ceríaco
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dmitry Dmitriev
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Neal Evenhuis
- Department of Natural Sciences, Bernice Pauahi Bishop Museum, Honolulu, Hawaii, United States of America
| | - Mark J. Grygier
- National Museum of Marine Biology and Aquarium, Checheng, Taiwan
| | - Mark S. Harvey
- Department of Terrestrial Zoology, Western Australian Museum, Welshpool DC, Australia
| | | | - Nikita Kluge
- Department of Entomology, Saint-Petersburg State University, Saint Petersburg, Russia
| | - Frank-T. Krell
- Denver Museum of Nature and Science, Denver, Colorado, United States of America
| | - Jun-ichi Kojima
- Natural History Laboratory, Faculty of Science, Ibaraki University, Mito, Japan
| | - Sven O. Kullander
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Paulo Lucinda
- Laboratório de Ictiologia Sistemática, Universidade Federal do Tocantins, Tocantins, Brazil
| | | | - Cristina Luisa Scioscia
- Arachnology Division, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’, Buenos Aires, Argentina
| | - Daniel Whitmore
- Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Douglas Yanega
- Department of Entomology, University of California, Riverside, Riverside, California, United States of America
| | - Zhi-Qiang Zhang
- Manaaki Whenua–Landcare Research, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Hong-Zhang Zhou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Thomas Pape
- Zoological Museum, Natural History Museum of Denmark, Copenhagen, Denmark
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14
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Wilson AW, Eberhardt U, Nguyen N, Noffsinger CR, Swenie RA, Loucks JL, Perry BA, Herrera M, Osmundson TW, DeLong-Duhon S, Beker HJ, Mueller GM. Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera. J Fungi (Basel) 2023; 9:788. [PMID: 37623559 PMCID: PMC10455624 DOI: 10.3390/jof9080788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/13/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023] Open
Abstract
The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of "splitting" taxa into numerous taxonomic units produces greater barcode gaps when compared to "lumping". The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species.
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Affiliation(s)
| | - Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Nhu Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawaiʻi at Mānoa, 3190 Maile Way, St. John 102, Honolulu, HI 96822, USA
| | - Chance R. Noffsinger
- Department of Ecology and Evolutionary Biology, University of Tennessee, Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996, USA
| | - Rachel A. Swenie
- Department of Ecology and Evolutionary Biology, University of Tennessee, Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996, USA
| | | | - Brian A. Perry
- Department of Biological Sciences, California State University East Bay, 25800 Carlos Bee Blvd., Hayward, CA 94542, USA
| | - Mariana Herrera
- Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA
| | - Todd W. Osmundson
- Biology Department, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, USA
| | | | - Henry J. Beker
- Royal Holloway College, University of London, London WC1E 7HU, UK
- Plantentuin Meise, Nieuwelaan 38, B-1860 Meise, Belgium
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15
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Gao Y, Zhong T, Bhat JD, Gomes de Farias AR, Dawoud TM, Hyde KD, Xiong W, Li Y, Gui H, Yang X, Wu S, Wanasinghe DN. Pleomorphic Dematiomelanommayunnanense gen. et sp. nov. (Ascomycota, Melanommataceae) from grassland vegetation in Yunnan, China. MycoKeys 2023; 98:273-297. [PMID: 37539358 PMCID: PMC10394607 DOI: 10.3897/mycokeys.98.107093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
During a survey of microfungi associated with grasslands and related vegetation types from Yunnan Province in China, various ascomycetous and coelomycetous fungi were isolated. This study reports the discovery of four strains of ascomycetous and coelomycetous fungi from dead stalks of Hypericummonogynum L. (Hypericaceae) and Rubusparvifolius L. (Rosaceae) in the Zhaotong region of Yunnan Province, China. The isolates were characterized using multi-locus phylogenetic analyses and were found to represent a new monophyletic lineage in Melanommataceae (Pleosporales, Dothideomycetes). This new clade was named as Dematiomelanommayunnanense gen. et sp. nov. which consists of both sexual and asexual morphs. The sexual morph is characterized by globose to subglobose ascomata with a central ostiole, cylindrical asci with a pedicel and ocular chamber, and muriform, ellipsoidal to fusiform ascospores. The asexual morph has synanamorphs including both brown, muriform macroconidia and hyaline, round to oblong or ellipsoidal microconidia. These findings contribute to the understanding of fungal diversity in grasslands and related vegetation types in Yunnan Province, China.
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Affiliation(s)
- Ying Gao
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, ChinaCenter for Mountain Futures, Kunming Institute of BotanyKunmingChina
- School of Science, Mae Fah Luang University, Chiang Rai 57100, ThailandMae Fah Luang UniversityChiang RaiThailand
| | - Tingfang Zhong
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, ThailandKey Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Jayarama D. Bhat
- University of Chinese Academy of Sciences, Beijing 100049, ChinaKing Saud UniversityRiyadhSaudi Arabia
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh-11451, Saudi ArabiaVishnugupta VishwavidyapeetamGokarnaIndia
| | | | - Turki M. Dawoud
- University of Chinese Academy of Sciences, Beijing 100049, ChinaKing Saud UniversityRiyadhSaudi Arabia
| | - Kevin D. Hyde
- School of Science, Mae Fah Luang University, Chiang Rai 57100, ThailandMae Fah Luang UniversityChiang RaiThailand
| | - Weiqiang Xiong
- Biology Division, Vishnugupta Vishwavidyapeetam, Ashoke, Gokarna 581326, IndiaScience and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace ChemotechnologyHubeiChina
| | - Yunju Li
- Science and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace Chemotechnology, Xiangyang, 441003, Hubei, ChinaThe State Phosphorus Resource Development and Utilization Engineering Technology Research CentreKunmingChina
- The State Phosphorus Resource Development and Utilization Engineering Technology Research Centre, Yunnan Phosphate Chemical Group Co. Ltd, Kunming, ChinaYTH Modern Agriculture Development Co. LtdKunmingChina
| | - Heng Gui
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, ChinaCenter for Mountain Futures, Kunming Institute of BotanyKunmingChina
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, ThailandKey Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Xuefei Yang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, ThailandKey Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Shixi Wu
- Biology Division, Vishnugupta Vishwavidyapeetam, Ashoke, Gokarna 581326, IndiaScience and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace ChemotechnologyHubeiChina
| | - Dhanushka N. Wanasinghe
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, ThailandKey Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- YTH Modern Agriculture Development Co. Ltd, Kunming, ChinaCenter for Mountain Futures, Kunming Institute of BotanyYunnanChina
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16
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Zhang ZY, Feng Y, Tong SQ, Ding CY, Tao G, Han YF. Morphological and phylogenetic characterisation of two new soil-borne fungal taxa belonging to Clavicipitaceae (Hypocreales, Ascomycota). MycoKeys 2023; 98:113-132. [PMID: 37324546 PMCID: PMC10267719 DOI: 10.3897/mycokeys.98.106240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/27/2023] [Indexed: 06/17/2023] Open
Abstract
The fungal taxa belonging to the Clavicipitaceae (Hypocreales, Ascomycota) are widely distributed and include diverse saprophytic, symbiotic and pathogenic species that are associated with soils, insects, plants, fungi and invertebrates. In this study, we identified two new fungal taxa belonging to the family Clavicipitaceae that were isolated from soils collected in China. Morphological characterisation and phylogenetic analyses showed that the two species belong to Pochonia (Pochoniasinensissp. nov.) and a new genus for which we propose Paraneoaraneomycesgen. nov. in Clavicipitaceae.
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Affiliation(s)
- Zhi-Yuan Zhang
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang 550025, ChinaGuizhou Minzu UniversityGuiyangChina
| | - Yao Feng
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang 550025, ChinaGuizhou Minzu UniversityGuiyangChina
| | - Shuo-Qiu Tong
- School of Chinese Ethnic Medicine, Guizhou Minzu University, Guiyang, Guizhou, 550025, ChinaGuizhou UniversityGuiyangChina
| | - Chen-Yu Ding
- School of Chinese Ethnic Medicine, Guizhou Minzu University, Guiyang, Guizhou, 550025, ChinaGuizhou UniversityGuiyangChina
| | - Gang Tao
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang 550025, ChinaGuizhou Minzu UniversityGuiyangChina
| | - Yan-Feng Han
- School of Chinese Ethnic Medicine, Guizhou Minzu University, Guiyang, Guizhou, 550025, ChinaGuizhou UniversityGuiyangChina
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17
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The chalara-like anamorphs of Leotiomycetes. FUNGAL DIVERS 2023. [DOI: 10.1007/s13225-023-00515-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
AbstractThe chalara-like anamorphs of Leotiomycetes are phialidic hyphomycetes with cylindrical collarettes and deeply seated sporulating loci, and hyaline, aseptate or septate, cylindrical conidia. They are commonly found on plant litters in both terrestrial and submerged environments, and with broad geographical distribution. This paper reports our research result of diversity, taxonomy and phylogeny of these fungi in China, which is based on a systematic study by using an integrated approach of literature study, morphological observation and phylogenetic analyses of 153 chalara-like fungal species with diversified morphology in conidiomata, setae, conidiophores, phialides and conidia. The phylogenetic analyses employing different datasets of SSU, LSU and ITS sequences of 116 species showed that these chalara-like fungi were paraphyletic and scattered in 20 accepted genera belonging to five families of Leotiomycetes: Arachnopezizaceae, Hamatocanthoscyphaceae, Helotiaceae, Neolauriomycetaceae and Pezizellaceae. Additional six genera, Ascoconidium, Bioscypha, Chalarodendron, Didonia, Phaeoscypha and Tapesina, all reported with chalara-like anamorphs in literatures, are also accepted as members of Pezizellaceae or Leotiomycetes genera incertae sedis. Among of these 26 accepted genera of chalara-like fungi in Leotiomycetes, 17 genera are asexually typified genera (Ascoconidium, Bloxamia, Chalara, Chalarodendron, Constrictochalara, Cylindrochalara, Cylindrocephalum, Leochalara, Lareunionomyces, Minichalara, Neochalara, Neolauriomyces, Nagrajchalara, Parachalara, Stipitochalara, Xenochalara and Zymochalara), and 9 are sexually typified genera (Bioscypha, Bloxamiella, Calycellina, Calycina, Didonia, Hymenoscyphus, Mollisina, Phaeoscypha and Tapesina). The phylogenetic significance of conidial septation in generic delimitation was further confirmed; while other morphologies such as conidiomata, setae, conidiophores, phialides, conidial length, and conidial ornamentation have little phylogenetic significance, but could be used for species delimitation. The polyphyletic genus Chalara s. lat. is revised with monophyletic generic concepts by redelimitation of Chalara s. str. in a narrow concept, adaption of the emended Calycina to also include asexually typified chalara-like fungi, reinstatement of Cylindrocephalum, and introduction of six new genera: Constrictochalara W.P. Wu & Y.Z. Diao, Leochalara W.P. Wu & Y.Z. Diao, Minichalara W.P. Wu & Y.Z. Diao, Nagrajchalara W.P. Wu & Y.Z. Diao, Parachalara W.P. Wu & Y.Z. Diao and Stipitochalara W.P. Wu & Y.Z. Diao. Chaetochalara becomes a synonym of Chalara s. str., and the known species are disassembled into Chalara s. str. and Nagrajchalara. The polyphyletic genus Bloxamia is also redefined by introducing the new genus Bloxamiella W.P. Wu & Y.Z. Diao for B. cyatheicola. Five existing species of Chalara s. lat. were excluded from Leotiomycetes and reclassified: Chalara breviclavata as Chalarosphaeria breviclavata W.P. Wu & Y.Z. Diao gen. et sp. nov. in Chaetosphaeriaceae, C. vaccinii as Sordariochalara vaccinii W.P. Wu & Y.Z. Diao gen. et sp. nov. in Lasiosphaeriaceae, and three other Chalara species with hyaline phialides, C. hyalina, C. schoenoplecti and C. siamense as combinations of Pyxidiophora in Pyxidiophoraceae. For biodiversity of these fungi in China, a total of 80 species in 12 genera, including 60 new species, 17 new records and 1 new name, were discovered and documented in this paper. In addition, five species including three new species are reported from Japan. In connection to this revision, a total of 44 new combinations are made. The identification keys are provided for most of these genera. Future research area of these fungi should be the phylogenetic relationship of several sexually typified genera such as Bioscypha, Calycellina, Calycina, Didonia, Phaeoscypha, Rodwayella and Tapesina, and systematic revision of existing names under the genera Bloxamia, Chaetochalara and Chalara.
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18
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Culturable Diversity of Lichen-Associated Yeasts through Enrichment Strategies. ECOLOGIES 2023. [DOI: 10.3390/ecologies4010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Lichens are symbiotic partnerships between a filamentous fungus and a photosymbiotic “alga”. Studies show that lichens harbor endothallic fungi, but that some taxa have been difficult to isolate from the main filamentous thallus-forming fungus and other faster growing lichenicolous/endothallic fungi. Therefore, we aimed to develop and evaluate liquid yeast-enrichment strategies to (1) isolate lichen-associated yeasts in pure culture, and (2) determine the taxonomic placement and breadth of the diversity of culturable yeasts. Eighty-two lichen samples were collected and washed with distilled water, and healthy thalli were ground up and added to seven different yeast-enrichment broths. Yeast colonies were isolated in pure culture and identified using molecular techniques. Initial isolates were identified using BLASTn analysis, and a taxonomic refinement was completed using PhyML analysis. In total, 215 isolates were obtained. The most prevalently isolated ascomycetous yeasts were within the Dothideomycetes (Aureobasidium, Plowrightia, and Dothiora), while the most frequently isolated basidiomycetous yeasts belonged to the genera Curvibasidium, Sporobolomyces, and Tremella. The generic placements could not be determined for 17 isolates, and in total 25 novel species were recovered. The results of this research indicate that (1) lichen-associated yeasts are diverse, (2) employing liquid enrichment strategies is effective for isolating many of these, and (3) lichen thalli represent a valuable untapped reservoir of diverse and novel yeast species.
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Zhou LW, May TW. Fungal taxonomy: current status and research agendas for the interdisciplinary and globalisation era. Mycology 2023; 14:52-59. [PMID: 36816771 PMCID: PMC9930751 DOI: 10.1080/21501203.2022.2103194] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
Abstract
Fungal taxonomy is a fundamental discipline that aims to recognise all fungi and their kinships. Approximately 5% of a practical estimate of 2.2-3.8 million species globally are currently known, and consequently the Fungal Tree of Life (FTOL) is very incompletely reconstructed. With the advances of new technologies, mycology is marching into the interdisciplinary and globalisation era. To make fungal taxonomy relevant, innovative sampling methods and phylogenomics analyses should be performed to reconstruct a much more comprehensive FTOL. In association with this densely sampled FTOL, multiomics will reveal what drives fungal species diversification and how fungal traits evolve to adapt to various environments, while metagenomics will facilitate the understanding and protection of the ecological functions of fungi. A coordinated approach to pursuing these research agendas that includes conceiving of and costing a mission to describe all the fungi on the planet will unlock potential of fungi to support sustainable development of our society.
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Affiliation(s)
- Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,CONTACT Li-Wei Zhou
| | - Tom W. May
- Royal Botanic Gardens Victoria, Melbourne, Australia,Tom W. May
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Cordeiro TRL, Walther G, Lee HB, Nguyen TTT, de Souza CAF, Lima DX, de Oliveira RJV, Góes-Neto A, Tomé LMR, Kurzai O, Voigt K, de Azevedo Santiago ALCM. A polyphasic approach to the taxonomy of Backusella reveals two new species. Mycol Prog 2023. [DOI: 10.1007/s11557-023-01864-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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21
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Dong JH, Zhang XC, Chen JJ, Zhu ZL, Zhao CL. A phylogenetic and taxonomic study on Steccherinum (Polyporales, Basidiomycota): Focusing on three new Steccherinum species from southern China. Front Cell Infect Microbiol 2023. [DOI: 10.3389/fcimb.2023.1103579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The wood-inhabiting fungi play an integral role in wood degradation and the cycle of matter in the ecological system. They are considered as the “key player” in wood decomposition, because of their ability to produce all kinds of enzymes that break down woody lignin, cellulose and hemicellulose. In the present study, three new wood-inhabiting fungal species, Steccherinum fissurutum, S. punctatum and S. subtropicum spp. nov., collected from southern China, are proposed based on a combination of morphological features and molecular evidence. Steccherinum fissurutum is characterized by the resupinate, subceraceous basidiomata with cracked hymenophore, a monomitic hyphal system with clamped generative hyphae and cylindrical basidiospores; S. punctatum is characterized by the annual, punctate basidiomata with leathery hymenophore, cylindrical, strongly encrusted cystidia and ellipsoid basidiospores (3.6–4.5 ×2.6–3.4 µm); S. subtropicum is characterized by its effuse-reflexed basidiomata, a odontioid hymenophore with pink to lilac hymenial surface and ellipsoid basidiospores measuring as (2.8–3.4 × 2.0–2.7 µm). Sequences of ITS and nLSU rRNA markers of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. The ITS+nLSU analysis of the family Steccherinaceae indicated that the three new species clustered into the genus Steccherinum. Based on further analysis of ITS+nLSU dataset, the phylogenetic analysis confirmed that S. subtropicum was sister to S. enuispinum; S. fissurutum formed a monophyletic lineage; S. punctatum grouped with a clade comprised S. straminellum and S. ciliolatum.
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Dong JH, Zhang XC, Chen JJ, Zhu ZL, Zhao CL. A phylogenetic and taxonomic study on Steccherinum (Polyporales, Basidiomycota): Focusing on three new Steccherinum species from southern China. Front Cell Infect Microbiol 2023; 12:1103579. [PMID: 36817691 PMCID: PMC9930103 DOI: 10.3389/fcimb.2022.1103579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 12/22/2022] [Indexed: 01/28/2023] Open
Abstract
The wood-inhabiting fungi play an integral role in wood degradation and the cycle of matter in the ecological system. They are considered as the "key player" in wood decomposition, because of their ability to produce all kinds of enzymes that break down woody lignin, cellulose and hemicellulose. In the present study, three new wood-inhabiting fungal species, Steccherinum fissurutum, S. punctatum and S. subtropicum spp. nov., collected from southern China, are proposed based on a combination of morphological features and molecular evidence. Steccherinum fissurutum is characterized by the resupinate, subceraceous basidiomata with cracked hymenophore, a monomitic hyphal system with clamped generative hyphae and cylindrical basidiospores; S. punctatum is characterized by the annual, punctate basidiomata with leathery hymenophore, cylindrical, strongly encrusted cystidia and ellipsoid basidiospores (3.6-4.5 ×2.6-3.4 µm); S. subtropicum is characterized by its effuse-reflexed basidiomata, a odontioid hymenophore with pink to lilac hymenial surface and ellipsoid basidiospores measuring as (2.8-3.4 × 2.0-2.7 µm). Sequences of ITS and nLSU rRNA markers of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. The ITS+nLSU analysis of the family Steccherinaceae indicated that the three new species clustered into the genus Steccherinum. Based on further analysis of ITS+nLSU dataset, the phylogenetic analysis confirmed that S. subtropicum was sister to S. enuispinum; S. fissurutum formed a monophyletic lineage; S. punctatum grouped with a clade comprised S. straminellum and S. ciliolatum.
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Affiliation(s)
- Jun-Hong Dong
- Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, China,College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Xun-Chi Zhang
- Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, China,College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Jia-Jia Chen
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Zhong-Long Zhu
- College of Forestry, Beijing Forestry University, Beijing, China,*Correspondence: Chang-Lin Zhao, ; Zhong-Long Zhu,
| | - Chang-Lin Zhao
- Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, China,College of Biodiversity Conservation, Southwest Forestry University, Kunming, China,Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China,*Correspondence: Chang-Lin Zhao, ; Zhong-Long Zhu,
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Hawksworth DL. MycoNews 2022: editorial, news, reports, awards, personalia, and book news. IMA Fungus 2023; 14:1. [PMID: 36624519 PMCID: PMC9828352 DOI: 10.1186/s43008-022-00106-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
This fourth annual edition of MycoNews starts with an editorial asking if mycology is approaching a tipping point, and note of the journal's 2021 Impact Factor almost doubling from 2020. Updated information and new speakers for IMC12 in 2024 is presented. Reports are provided for the Rise of the Fungi symposium in Amsterdam and of MycoRiseUP! in Warsaw in 2022. Information on activities of the International Commission on the Taxonomy of Fungi (ICTF) in the last two years are presented, including the formation of new Working Groups. Procedures for the nomination of IMA awards and for nomenclature proposals to be presented at IMC12 are provided. The Westerdijk Institute awards to Feng-Yan Bai and Marc Stadler are recorded, and Michael Wingfield and Geoffrey Kibby are congratulated on special awards they have received. Tributes are paid to the passing of two distinguished mycologists during the year, John Parmelee and John Pitt. Reviews of six mycological books published in 2021-22 are also provided.
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Affiliation(s)
- David L. Hawksworth
- grid.4903.e0000 0001 2097 4353Trait Diversity and Function, Royal Botanic Gardens, Kew, TW9 3DS Surrey UK ,grid.35937.3b0000 0001 2270 9879Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK ,grid.464353.30000 0000 9888 756XJilin Agricultural University, Changchun, 130118 Jilin Province China ,grid.5491.90000 0004 1936 9297Geography and Environmental Science, University of Southampton, Highfield Campus, Southampton, SO17 1BJ UK
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Toghueo RMK, Vázquez de Aldana BR, Zabalgogeazcoa I. Diaporthe species associated with the maritime grass Festuca rubra subsp. pruinosa. Front Microbiol 2023; 14:1105299. [PMID: 36876098 PMCID: PMC9978114 DOI: 10.3389/fmicb.2023.1105299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
Festuca rubra subsp. pruinosa is a perennial grass growing in sea cliffs where plants are highly exposed to salinity and marine winds, and often grow in rock fissures where soil is absent. Diaporthe species are one of the most abundant components of the root microbiome of this grass and several Diaporthe isolates have been found to produce beneficial effects in their host and other plant species of agronomic importance. In this study, 22 strains of Diaporthe isolated as endophytes from roots of Festuca rubra subsp. pruinosa were characterized by molecular, morphological, and biochemical analyses. Sequences of the nuclear ribosomal internal transcribed spacers (ITS), translation elongation factor 1-α (TEF1), beta-tubulin (TUB), histone-3 (HIS), and calmodulin (CAL) genes were analyzed to identify the isolates. A multi-locus phylogenetic analysis of the combined five gene regions led to the identification of two new species named Diaporthe atlantica and Diaporthe iberica. Diaporthe atlantica is the most abundant Diaporthe species in its host plant, and Diaporthe iberica was also isolated from Celtica gigantea, another grass species growing in semiarid inland habitats. An in vitro biochemical characterization showed that all cultures of D. atlantica produced indole-3-acetic acid and ammonium, and the strains of D. iberica produced indole 3-acetic acid, ammonium, siderophores, and cellulase. Diaporthe atlantica is closely related to D. sclerotioides, a pathogen of cucurbits, and caused a growth reduction when inoculated in cucumber, melon, and watermelon.
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Affiliation(s)
- Rufin Marie Kouipou Toghueo
- Plant-Microorganism Interaction Research Group, Institute of Natural Resources and Agrobiology of Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Beatriz R Vázquez de Aldana
- Plant-Microorganism Interaction Research Group, Institute of Natural Resources and Agrobiology of Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - Iñigo Zabalgogeazcoa
- Plant-Microorganism Interaction Research Group, Institute of Natural Resources and Agrobiology of Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
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Ilyukhin E, Nguyen HDT, Castle AJ, Ellouze W. Cytospora paraplurivora sp. nov. isolated from orchards with fruit tree decline syndrome in Ontario, Canada. PLoS One 2023; 18:e0279490. [PMID: 36630368 PMCID: PMC9833554 DOI: 10.1371/journal.pone.0279490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 11/25/2022] [Indexed: 01/12/2023] Open
Abstract
A new species of Cytospora was isolated from cankered wood of Prunus spp. during a survey of orchards exhibiting symptoms of fruit tree decline syndrome in southern Ontario, Canada. We found isolates that are morphologically similar to species in the Cytosporaceae family, which is characterized by single or labyrinthine locules, filamentous conidiophores or clavate to elongate obovoid asci and allantoid, hyaline conidia. Multi-gene phylogenetic analysis of ITS, LSU, act and tef1- α showed that the isolates form a distinct clade, sister to Cytospora plurivora. Morphologically, our isolates showed differences in the length of conidia and culture characteristics compared to C. plurivora, suggesting the establishment of a new species. The species is described as Cytospora paraplurivora sp. nov. and placed in the family Cytosporaceae of Diaporthales. Additionally, we sequenced, assembled and characterized the genome of the representative isolate for this new species. The phylogenomic analysis confirms the species order and family level classification. C. paraplurivora sp. nov. has the potential to severely affect stone fruits production, causing cankers and dieback in stressed trees, and eventually leads to tree decline. Pathogenicity tests show that the species is pathogenic to Prunus persica var. persica.
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Affiliation(s)
- Evgeny Ilyukhin
- Agriculture and Agri-Food Canada, Vineland Station, Ontario, Canada
| | | | - Alan J. Castle
- Department of Biological Sciences, Brock University, St. Catharines, Canada
| | - Walid Ellouze
- Agriculture and Agri-Food Canada, Vineland Station, Ontario, Canada
- * E-mail:
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Haelewaters D, Gafforov Y, Zhou LW. Editorial: Biodiversity and conservation of fungi and fungus-like organisms. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:973249. [PMID: 37746196 PMCID: PMC10512388 DOI: 10.3389/ffunb.2022.973249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 11/21/2022] [Indexed: 09/26/2023]
Affiliation(s)
- Danny Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, Ghent, Belgium
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Yusufjon Gafforov
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of Republic of Uzbekistan, Tashkent, Uzbekistan
- AKFA University, Tashkent, Uzbekistan
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Deep Genotypic Species Delimitation of Aspergillus Section Flavi Isolated from Brazilian Foodstuffs and the Description of Aspergillus annui sp. nov. and Aspergillus saccharicola sp. nov. J Fungi (Basel) 2022; 8:jof8121279. [PMID: 36547612 PMCID: PMC9781283 DOI: 10.3390/jof8121279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Aspergillus section Flavi is a fungal group that is important in food because it contains spoilage and potentially aflatoxigenic species. Aflatoxins are metabolites that are harmful to human and animal health and have been recognized as the primary natural contaminant in food. Therefore, recognizing the biodiversity of this group in food is necessary to reduce risks to public health. Our study aimed to investigate the diversity of Aspergillus section Flavi isolated from Brazilian foodstuffs such as cassava, sugarcane, black pepper, paprika, Brazil nuts, yerba-mate, peanuts, rice, and corn. A polyphasic approach integrating phenotypic data and multilocus genotypic analyses (CaM, BenA, and RPB2) was performed for 396 strains. Two new species in the Aspergillus subgenus Circumdati section Flavi are proposed using maximum-likelihood analysis, Bayesian inference, and coalescence-based methods: Aspergillus saccharicola sp. nov. and Aspergillus annui sp. nov. A. saccharicola sp. nov. belongs to the series Flavi, is a potentially aflatoxigenic species (B1, B2, G1, and G2), closely related to Aspergillus arachidicola, and was found mostly in sugarcane. A. annui sp. nov. was isolated from samples of sweet paprika. To accommodate A. annui sp. nov., a new series Annuorum was proposed.
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Grupe II A, Smith M, Weier A, Healy R, Caiafa M, Pfister D, Haelewaters D, Quandt C. Two new species of Phaeohelotium ( Leotiomycetes: Helotiaceae) from Chile and their putative ectomycorrhizal status. Fungal Syst Evol 2022; 10:231-249. [PMID: 36741556 PMCID: PMC9875694 DOI: 10.3114/fuse.2022.10.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Species of the genus Phaeohelotium (Leotiomycetes: Helotiaceae) are cup fungi that grow on decaying wood, leaves, litter, and directly on soil. Northern Hemisphere species are primarily found on litter and wood, whereas in the Southern Hemisphere the genus includes a mix of saprotrophs as well as taxa that grow on soil in association with ectomycorrhizal trees. The diversity of this genus has not been fully explored in southern South America. Here we describe two species from Chile, Phaeohelotium maiusaurantium sp. nov. and Ph. pallidum sp. nov., found on soil in Patagonian Nothofagaceae-dominated forests. We present macro- and micromorphological descriptions, illustrations, and molecular phylogenetic analyses. The two new species are placed in Phaeohelotium with high support in our 15-locus phylogeny as well as phylogenetic reconstructions based on the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene. Our ITS phylogeny places both Ph. maiusaurantium and Ph. pallidum in a well-supported subclade that includes ectomycorrhizal root tip samples from Australasia. Similar species can be separated from these new taxa based on morphological characteristics, biogeography, substrate, and sequence data. In addition, two unnamed species from Chilean Nothofagaceae forests (Phaeohelotium sp. 1 and Phaeohelotium sp. 2) are documented from scant collections and sequence data and await description until more material becomes available. Citation: Grupe II AC, Smith ME, Weier A, Healy R, Caiafa MV, Pfister DH, Haelewaters D, Quandt CA (2022). Two new species of Phaeohelotium (Leotiomycetes: Helotiaceae) from Chile and their putative ectomycorrhizal status. Fungal Systematics and Evolution 10: 231-249. doi: 10.3114/fuse.2022.10.10.
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Affiliation(s)
- A.C. Grupe II
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - M.E. Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - A. Weier
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - R. Healy
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - M.V. Caiafa
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA
| | - D.H. Pfister
- Department of Organismic and Evolutionary Biology & Farlow Reference Library and Herbarium of Cryptogamic Botany, Harvard University, Cambridge MA 20138, USA
| | - D. Haelewaters
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
- Research Group Mycology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - C.A. Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA
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Ecological speciation of Japanese hedgehog mushroom: Hydnum subalpinum sp. nov. is distinguished from its sister species H. repando-orientale by means of integrative taxonomy. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01844-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Weldon WA, McGhee GC, Jones LA, Stockwell VO. Taxonomic Reclassification of the Fungal Pathogen Causing Dry Berry Disease of Caneberries into the Division Ascomycota as Monilinia rubi. PLANT DISEASE 2022; 106:2788-2796. [PMID: 35442057 DOI: 10.1094/pdis-11-21-2618-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As molecular genetic techniques improve and sequence data becomes available for more fungal species, taxonomic classifications historically based upon growth morphology alone are being revisited and occasionally reclassified. Herein, we present such an instance for the fungal pathogen that causes dry berry disease of caneberries. The organism was previously described as the basidiomycete fungus Rhizoctonia rubi based upon the pathogen's production of Rhizoctonia-like angular branching hyphae. Utilizing molecular genetic techniques unavailable when the pathogen was first characterized in 1959, three housekeeping gene regions (ITS, β-tubulin, and G3PDH) were sequenced across 13 contemporary dry berry isolates, as well as the original 1959 R. rubi type strain, CBS382.59. The resulting neighbor-joining, maximum likelihood, and Bayesian phylogenies for single and multilocus sequences provide strong evidence that the dry berry pathogen was misclassified. This data, in addition to revisiting in vivo macroscopic and microscopic growth morphology, again comparing contemporary dry berry isolates to the CBS382.59 type strain, suggests that the causal organism is a new species within the genus Monilinia that we propose be classified as Monilinia rubi. A transition from designation as a basidiomycete fungus to an ascomycete fungus could have implications on chemical management decisions, as well as the assumptions made about cell structure and the pathogen's putative life cycle.
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Affiliation(s)
| | - Gayle C McGhee
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97330
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Wang F, Wang K, Cai L, Zhao M, Kirk PM, Fan G, Sun Q, Li B, Wang S, Yu Z, Han D, Ma J, Wu L, Yao Y. Fungal names: a comprehensive nomenclatural repository and knowledge base for fungal taxonomy. Nucleic Acids Res 2022; 51:D708-D716. [PMID: 36271801 PMCID: PMC9825588 DOI: 10.1093/nar/gkac926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/14/2022] [Accepted: 10/07/2022] [Indexed: 01/30/2023] Open
Abstract
Fungal taxonomy is a complex and rapidly changing subject, which makes proper naming of fungi challenging for taxonomists. A registration platform with a standardized and information-integrated database is a powerful tool for efficient research on fungal taxonomy. Fungal Names (FN, https://nmdc.cn/fungalnames/; launched in 2011) is one of the three official fungal nomenclatural repositories authorized by the International Nomenclature Committee for Fungi (NCF). Currently, FN includes >567 000 taxon names from >10 000 related journals and books published since 1596 and covers >147 000 collection records of type specimens/illustrations from >5000 preserving agencies. FN is also a knowledge base that integrates nomenclature information with specimens, culture collections and herbaria/fungaria, publications and taxonomists, and represents a summary of the history and recent advances in fungal taxonomy. Published fungal names are categorized based on well-accepted nomenclature rules and can be readily searched with different keywords and strategies. In combination with a standardized name checking tool and a sequence alignment-based identification package, FN makes the registration and typification of nomenclatural novelties of fungi convenient and accurate.
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Affiliation(s)
| | | | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingjun Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Paul M Kirk
- Jodrell Laboratory, Royal Botanical Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Guomei Fan
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Qinglan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Bo Li
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Shuai Wang
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Zhengfei Yu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Dong Han
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Juncai Ma
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Linhuan Wu
- To whom correspondence should be addressed. Tel: +86 10 64807385;
| | - Yijian Yao
- Correspondence may also be addressed to Yijian Yao. Tel: 86 10 64807595;
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Seo CW, Kim SH, Lim YW, Park MS. Re-Identification on Korean Penicillium Sequences in GenBank Collected by Software GenMine. MYCOBIOLOGY 2022; 50:231-237. [PMID: 36158042 PMCID: PMC9467555 DOI: 10.1080/12298093.2022.2116816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/16/2022] [Accepted: 08/21/2022] [Indexed: 06/16/2023]
Abstract
Penicillium species have been actively studied in various fields, and many new and unrecorded species continue to be reported in Korea. Moreover, unidentified and misidentified Korean Penicillium species still exist in GenBank. Therefore, it is necessary to revise the Korean Penicillium inventory based on accurate identification. We collected Korean Penicillium nucleotide sequence records from GenBank using the newly developed software, GenMine, and re-identified Korean Penicillium based on the maximum likelihood trees. A total of 1681 Korean Penicillium GenBank nucleotide sequence records were collected from GenBank. In these records, 1208 strains with four major genes (Internal Transcribed Spacer rDNA region, β-tubulin, Calmodulin and RNA polymerase II) were selected for Penicillium re-identification. Among 1208 strains, 927 were identified, 82 were identified as other genera, the rest remained undetermined due to low phylogenetic resolution. Identified strains consisted of 206 Penicillium species, including 156 recorded species and 50 new species candidates. However, 37 species recorded in the national list of species in Korea were not found in GenBank. Further studies on the presence or absence of these species are required through literature investigation, additional sampling, and sequencing. Our study can be the basis for updating the Korean Penicillium inventory.
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Affiliation(s)
- Chang Wan Seo
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Sung Hyun Kim
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Young Woon Lim
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Myung Soo Park
- Department of Crops and Forestry, Korea National University of Agriculture and Fisheries, Jeonju, South Korea
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Abstract
AbstractThe classification of taxa belonging to the Sordariales has been problematic over the years. With the beginning of the DNA era, ascospore morphology, which was the main criterium for the delimitation of taxa in the Sordariales, was demonstrated to not be useful for inferring taxonomic relationships especially at the genus level. In the past decades, the combination of both morphological and molecular data allowed the reclassification of these taxa. Recently, a study of some often overlooked Diaporthomycetidae and Sordariomycetidae included a new taxonomic classification for members of the Sordariales, many of which were based on nomenclatural errors or which lacked sufficient data to support their hypotheses. The authors did not contribute any new DNA sequences, but instead relied on datasets generated by previous authors in their published phylogenetic studies. Surprisingly, different results were obtained contradicting these previous studies and, in an act of taxonomic vandalism, five new families were introduced without performing further molecular analyses to verify the incongruencies with these previous studies. Three of these new families, which we consider doubtful, are Bombardiaceae, Lasiosphaeridaceae and Zygospermellaceae. The family Strattoniaceae is here considered superfluous since it was introduced to accommodate only a single genus and delimited based on a species that is not the type species of Strattonia. The Neoschizotheciaceae was erected based on the new genus Neoschizothecium, which was introduced to accommodate members of Schizothecium since Huang et al. (2021) considered Schizothecium as a synonym of Podospora after misinterpreting their type species as the same. However, Schizothecium and Podospora have been two independent genera based on two different type species for half a century, making Neoschizothecium and Neoschizotheciaceae superfluous. Moreover, they proposed 32 new combinations, 16 of which are now superfluous or doubtful. Most of these taxonomic errors could have been avoided if a proper literature review had been performed. Two examples are the new superfluous combinations of Triangularia tarvisina and Cladorrhinum olerum, because the former is considered conspecific with Triangularia setosa, and the latter conspecific with Cladorrhinum foecundissimum, the anamorph of Arnium olerum. The focus of the current review is to provide a scientifically responsible alternative to the erroneous novelties proposed at the family, genus and species level in the recent classification of Sordariales.
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Amplicon Sequencing Reveals Novel Fungal Species Responsible for a Controversial Tea Disease. J Fungi (Basel) 2022; 8:jof8080782. [PMID: 35893150 PMCID: PMC9394346 DOI: 10.3390/jof8080782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 12/10/2022] Open
Abstract
Amplicon sequencing is a powerful tool for analyzing the fungal composition inside plants, whereas its application for the identification of etiology for plant diseases remains undetermined. Here, we utilize this strategy to clarify the etiology responsible for tea leaf brown-black spot disease (LBSD), a noticeable disease infecting tea plants etiology that remains controversial. Based on the ITS-based amplicon sequencing analysis, Didymella species were identified as separate from Pestalotiopsis spp. and Cercospora sp., which are concluded as the etiological agents. This was further confirmed by the fungal isolation and their specific pathogenicity on diverse tea varieties. Based on the morphologies and phylogenetic analysis constructed with multi-loci (ITS, LSU, tub2, and rpb2), two novel Didymella species—tentatively named D. theae and D. theifolia as reference to their host plants—were proposed and characterized. Here, we present an integrated approach of ITS-based amplicon sequencing in combination with fungal isolation and fulfillment of Koch’s postulates for etiological identification of tea plant disease, revealing new etiology for LBSD. This contributes useful information for further etiological identification of plant disease based on amplicon sequencing, as well as understanding, prevention, and management of this economically important disease.
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Ilyukhin E, Markovskaja S, Elgorban AM, Al-Rejaie SS, Maharachchikumbura SS. Genomic Characteristics and Comparative Genomics Analysis of Parafenestella ontariensis sp. nov. J Fungi (Basel) 2022; 8:jof8070732. [PMID: 35887487 PMCID: PMC9318755 DOI: 10.3390/jof8070732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
A new ascomycetous species of Parafenestella was isolated from Acer negundo during the survey of diseased trees in Southern Ontario, Canada. The species is morphologically similar to other taxa of Cucurbitariacea (Pleosporales). The new species is different from the extant species in the morphology of ascospores, culture characteristics and molecular data. The novel species is described as Parafenestella ontariensis sp. nov. based on morphological and multi-gene phylogenetic analyses using a combined set of ITS, LSU, tef1 and tub2 loci. Additionally, the genome of P. ontariensis was sequenced and analyzed. The phylogenomic analysis confirmed the close relationship of the species to the fenestelloid clades of Cucurbitariaceae. The comparative genomics analysis revealed that the species lifestyle appears to be multitrophic (necrotrophic or hemi-biotrophic) with a capability to turn pathogenic on a corresponding plant host.
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Affiliation(s)
- Evgeny Ilyukhin
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
- Correspondence: or
| | | | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Salim S. Al-Rejaie
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Sajeewa S.N. Maharachchikumbura
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China;
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Elshahed MS, Hanafy RA, Cheng Y, Dagar SS, Edwards JE, Flad V, Fliegerová KO, Griffith GW, Kittelmann S, Lebuhn M, O'Malley MA, Podmirseg SM, Solomon KV, Vinzelj J, Young D, Youssef NH. Characterization and rank assignment criteria for the anaerobic fungi (Neocallimastigomycota). Int J Syst Evol Microbiol 2022; 72. [PMID: 35852502 DOI: 10.1099/ijsem.0.005449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Establishing a solid taxonomic framework is crucial for enabling discovery and documentation efforts. This ensures effective communication between scientists as well as reproducibility of results between laboratories, and facilitates the exchange and preservation of biological material. Such framework can only be achieved by establishing clear criteria for taxa characterization and rank assignment. Within the anaerobic fungi (phylum Neocallimastigomycota), the need for such criteria is especially vital. Difficulties associated with their isolation, maintenance and long-term storage often result in limited availability and loss of previously described taxa. To this end, we provide here a list of morphological, microscopic, phylogenetic and phenotypic criteria for assessment and documentation when characterizing newly obtained Neocallimastigomycota isolates. We also recommend a polyphasic rank-assignment scheme for novel genus-, species- and strain-level designations for newly obtained Neocallimastigomycota isolates.
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Affiliation(s)
- Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA, USA
| | - Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA, USA
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark DE, USA
| | - Yanfen Cheng
- College of Animal Science and Technology, Nanjing Agricultural University., Nanjing, Jiangsu, PR China
| | - Sumit S Dagar
- Bioenergy Group, Agharkar Research Institute, Pune, India
| | | | - Veronika Flad
- Bavarian State Research Center for Agriculture (LfL), Central Department for Quality Assurance and Analytics, 85354 Freising, Germany
| | | | - Gareth W Griffith
- Institute of Biological, Environmental, and Rural Sciences (IBERS) Aberystwyth University, Aberystwyth, Wales, UK
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Michael Lebuhn
- Bavarian State Research Center for Agriculture (LfL), Central Department for Quality Assurance and Analytics, 85354 Freising, Germany
| | - Michelle A O'Malley
- Department of Chemical Engineering, Center for Bioengineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Sabine Marie Podmirseg
- Department of Microbiology, University of Innsbruck, Technikerstraße, Innsbruck, Austria
| | - Kevin V Solomon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark DE, USA
| | - Julia Vinzelj
- Department of Microbiology, University of Innsbruck, Technikerstraße, Innsbruck, Austria
| | - Diana Young
- Bavarian State Research Center for Agriculture (LfL), Central Department for Quality Assurance and Analytics, 85354 Freising, Germany
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA, USA
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Salgado-Salazar C, Thines M. Two new species of Plasmopara affecting wild grapes in the USA. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01813-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kennedy AH, Schoch CL, Marrero G, Brover V, Robbertse B. Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in Colletotrichum. PLANT DISEASE 2022; 106:1573-1596. [PMID: 35538602 PMCID: PMC9196201 DOI: 10.1094/pdis-09-21-2083-sr] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Publicly available and validated DNA reference sequences useful for phylogeny estimation and identification of fungal pathogens are an increasingly important resource in the efforts of plant protection organizations to facilitate safe international trade of agricultural commodities. Colletotrichum species are among the most frequently encountered and regulated plant pathogens at U.S. ports-of-entry. The RefSeq Targeted Loci (RTL) project at NCBI (BioProject no. PRJNA177353) contains a database of curated fungal internal transcribed spacer (ITS) sequences that interact extensively with NCBI Taxonomy, resulting in verified name-strain-sequence type associations for >12,000 species. We present a publicly available dataset of verified and curated name-type strain-sequence associations for all available Colletotrichum species. This includes an updated GenBank Taxonomy for 238 species associated with up to 11 protein coding loci and an updated RTL ITS dataset for 226 species. We demonstrate that several marker loci are well suited for phylogenetic inference and identification. We improve understanding of phylogenetic relationships among verified species, verify or improve phylogenetic circumscriptions of 14 species complexes, and reveal that determining relationships among these major clades will require additional data. We present detailed comparisons between phylogenetic and similarity-based approaches to species identification, revealing complex patterns among single marker loci that often lead to misidentification when based on single-locus similarity approaches. We also demonstrate that species-level identification is elusive for a subset of samples regardless of analytical approach, which may be explained by novel species diversity in our dataset and incomplete lineage sorting and lack of accumulated synapomorphies at these loci.
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Affiliation(s)
- Aaron H. Kennedy
- National Identification Services, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Beltsville, MD 20705
| | - Conrad L. Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Glorimar Marrero
- National Identification Services, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Beltsville, MD 20705
| | - Vyacheslav Brover
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
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Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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40
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Phukhamsakda C, Nilsson RH, Bhunjun CS, de Farias ARG, Sun YR, Wijesinghe SN, Raza M, Bao DF, Lu L, Tibpromma S, Dong W, Tennakoon DS, Tian XG, Xiong YR, Karunarathna SC, Cai L, Luo ZL, Wang Y, Manawasinghe IS, Camporesi E, Kirk PM, Promputtha I, Kuo CH, Su HY, Doilom M, Li Y, Fu YP, Hyde KD. The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00502-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractThe global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora, Bambusicola, Beltrania, Capronia, Distoseptispora, Endocalyx, Neocatenulostroma, Neodeightonia, Paraconiothyrium, Peroneutypa, Phaeoacremonium and Vanakripa. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.
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41
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Batista E, Lopes A, Alves A. How good are we at describing a new fungal species? A case study based on the family Botryosphaeriaceae (Dothideomycetes). Mycol Prog 2022. [DOI: 10.1007/s11557-022-01796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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Has taxonomic vandalism gone too far? A case study, the rise of the pay-to-publish model and the pitfalls of Morchella systematics. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01755-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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44
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Eberhardt U, Schütz N, Bartlett P, Hosaka K, Kasuya T, Beker HJ. Revisiting Hebeloma (Hymenogastraceae, Agaricales) in Japan: four species recombined into other genera but three new species discovered. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01757-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
AbstractHere, we present the results of studies of Japanese Hebeloma collections. The four species described by Imai as Hebeloma (H. fimicola, H. helvolescens, H. humosum, and H. tomoeae) are not from the genus Hebeloma, but are members of Agrocybe, Homophron, or Pholiota. Recombinations are made. Hebelomacrustuliniforme f. microspermum, described by Hongo, is a synonym of H. nanum. Three species of Hebeloma are described as new to science, all currently known only from Japan. Two of these species, H. asperosporum and H. cinnamomeum, are members of H. sect. Denudata while the third species H. citrisporum belongs to H. sect. Velutipes. Japanese records of H. cavipes, H. eburneum, H. hygrophilum, H. subtortum, and H. velutipes are validated. In total, fifteen species of Hebeloma are confirmed from Japan; this is compared with previous checklists.
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45
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Delgado G, Miller AN, Hashimoto A, Iida T, Ohkuma M, Okada G. A phylogenetic assessment of Endocalyx (Cainiaceae, Xylariales) with E. grossus comb. et stat. nov. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01759-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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46
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Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates. J Fungi (Basel) 2022; 8:jof8030226. [PMID: 35330228 PMCID: PMC8955040 DOI: 10.3390/jof8030226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/19/2022] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.
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Senanayake IC, Pem D, Rathnayaka AR, Wijesinghe SN, Tibpromma S, Wanasinghe DN, Phookamsak R, Kularathnage ND, Gomdola D, Harishchandra D, Dissanayake LS, Xiang MM, Ekanayaka AH, McKenzie EHC, Hyde KD, Zhang HX, Xie N. Predicting global numbers of teleomorphic ascomycetes. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00498-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AbstractSexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.
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Sun XR, Xu MY, Kong WL, Wu F, Zhang Y, Xie XL, Li DW, Wu XQ. Fine Identification and Classification of a Novel Beneficial Talaromyces Fungal Species from Masson Pine Rhizosphere Soil. J Fungi (Basel) 2022; 8:jof8020155. [PMID: 35205909 PMCID: PMC8877249 DOI: 10.3390/jof8020155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/16/2022] Open
Abstract
Rhizosphere fungi have the beneficial functions of promoting plant growth and protecting plants from pests and pathogens. In our preliminary study, rhizosphere fungus JP-NJ4 was obtained from the soil rhizosphere of Pinus massoniana and selected for further analyses to confirm its functions of phosphate solubilization and plant growth promotion. In order to comprehensively investigate the function of this strain, it is necessary to ascertain its taxonomic position. With the help of genealogical concordance phylogenetic species recognition (GCPSR) using five genes/regions (ITS, BenA, CaM, RPB1, and RPB2) as well as macro-morphological and micro-morphological characters, we accurately determined the classification status of strain JP-NJ4. The concatenated phylogenies of five (or four) gene regions and single gene phylogenetic trees (ITS, BenA, CaM, RPB1, and RPB2 genes) all show that strain JP-NJ4 clustered together with Talaromyces brevis and Talaromyces liani, but differ markedly in the genetic distance (in BenA gene) from type strain and multiple collections of T. brevis and T. liani. The morphology of JP-NJ4 largely matches the characteristics of genes Talaromyces, and the rich and specific morphological information provided by its colonies was different from that of T. brevis and T. liani. In addition, strain JP-NJ4 could produce reduced conidiophores consisting of solitary phialides. From molecular and phenotypic data, strain JP-NJ4 was identified as a putative novel Talaromyces fungal species, designated T. nanjingensis.
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Affiliation(s)
- Xiao-Rui Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.-R.S.); (M.-Y.X.); (W.-L.K.); (F.W.); (Y.Z.); (X.-L.X.)
| | - Ming-Ye Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.-R.S.); (M.-Y.X.); (W.-L.K.); (F.W.); (Y.Z.); (X.-L.X.)
| | - Wei-Liang Kong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.-R.S.); (M.-Y.X.); (W.-L.K.); (F.W.); (Y.Z.); (X.-L.X.)
| | - Fei Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.-R.S.); (M.-Y.X.); (W.-L.K.); (F.W.); (Y.Z.); (X.-L.X.)
| | - Yu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.-R.S.); (M.-Y.X.); (W.-L.K.); (F.W.); (Y.Z.); (X.-L.X.)
| | - Xing-Li Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.-R.S.); (M.-Y.X.); (W.-L.K.); (F.W.); (Y.Z.); (X.-L.X.)
| | - De-Wei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.-R.S.); (M.-Y.X.); (W.-L.K.); (F.W.); (Y.Z.); (X.-L.X.)
- The Connecticut Agricultural Experiment Station Valley Laboratory, Windsor, CT 06095, USA;
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.-R.S.); (M.-Y.X.); (W.-L.K.); (F.W.); (Y.Z.); (X.-L.X.)
- Correspondence:
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Torres-Garcia D, Gené J, García D. New and interesting species of Penicillium (Eurotiomycetes, Aspergillaceae) in freshwater sediments from Spain. MycoKeys 2022; 86:103-145. [PMID: 35145339 PMCID: PMC8825427 DOI: 10.3897/mycokeys.86.73861] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/10/2022] [Indexed: 11/12/2022] Open
Abstract
Penicillium species are common fungi found worldwide from diverse substrates, including soil, plant debris, food products and air. Their diversity in aquatic environments is still underexplored. With the aim to explore the fungal diversity in Spanish freshwater sediments, numerous Penicillium strains were isolated using various culture-dependent techniques. A preliminary sequence analysis of the β-tubulin (tub2) gene marker allowed us to identify several interesting species of Penicillium, which were later characterized phylogenetically with the barcodes recommended for species delimitation in the genus. Based on the multi-locus phylogeny of the internal transcribed spacer region (ITS) of the ribosomal DNA, and partial fragments of tub2, calmodulin (cmdA), and the RNA polymerase II largest subunit (rpb2) genes, in combination with phenotypic analyses, five novel species are described. These are P.ausonanum in sectionLanata-Divaricata, P.guarroi in sect.Gracilenta, P.irregulare in sect.Canescentia, P.sicoris in sect.Paradoxa and P.submersum in sect.Robsamsonia. The study of several isolates from samples collected in different locations resulted in the reinstatement of P.vaccaeorum into sectionCitrina. Finally, P.heteromorphum (sect.Exilicaulis) and P.tardochrysogenum (sect.Chrysogena) are reported, previously only known from Antarctica and China, respectively.
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Affiliation(s)
- Daniel Torres-Garcia
- Universitat Rovira i Virgili, Unitat de Micologia, Facultat de Medicina i Ciències de la Salut and IISPV, 43201-Reus, SpainUniversitat Rovira i VirgiliReusSpain
| | - Josepa Gené
- Universitat Rovira i Virgili, Unitat de Micologia, Facultat de Medicina i Ciències de la Salut and IISPV, 43201-Reus, SpainUniversitat Rovira i VirgiliReusSpain
| | - Dania García
- Universitat Rovira i Virgili, Unitat de Micologia, Facultat de Medicina i Ciències de la Salut and IISPV, 43201-Reus, SpainUniversitat Rovira i VirgiliReusSpain
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The haustorium as a driving force for speciation in thallus-forming Laboulbeniomycetes. IMA Fungus 2022; 13:1. [PMID: 35101145 PMCID: PMC8805332 DOI: 10.1186/s43008-021-00087-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/19/2021] [Indexed: 11/10/2022] Open
Abstract
Laboulbeniomycetes is a class of fungi that have obligate associations with arthropod hosts, either for dispersal (order Pyxidiophorales) or as biotrophic parasites (orders Herpomycetales and Laboulbeniales). Here, we focus on Herpomycetales and Laboulbeniales, which include fungi that form thalli, 3-dimensional, multicellular units of 1000 s of cells. Based on recently published data regarding patterns of speciation, we present the One-Host-One-Parasite model (1H1P) for haustorial thallus-forming Laboulbeniomycetes. We hypothesize that taxa with haustoria, rhizoidal structures that make contact with the host’s body cavity, have very strict host specificity. For taxa without haustoria, the microhabitat—as selected by the host—governs host shifting, presence or absence of the fungus, abundance, effective host range, and geographic distribution. We make suggestions for future research including fluorescent labeling of waxy lipids and mass spectrometry. These techniques have the potential to generate the data necessary to evaluate the here proposed 1H1P hypothesis for Herpomycetales and Laboulbeniales.
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