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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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Sun C, Liu YF, Liang YM, Wang L. Four new species of Puccinia from herbaceous plants in China. Mycologia 2024; 116:309-321. [PMID: 38252498 DOI: 10.1080/00275514.2023.2289697] [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: 11/30/2022] [Accepted: 11/27/2023] [Indexed: 01/24/2024]
Abstract
Members of Puccinia (Pucciniaceae, Pucciniales) are known as plant pathogens worldwide, which are characterized by their morphology, host association, and molecular data of various genes. In the present study, 10 specimens of Puccinia were collected from four herbaceous plants (Anaphalis hancockii, Anthriscus sylvestris, Halenia elliptica, and Pilea pumila) in China and identified based on morphology and phylogeny. As a result, 10 samples represent four undescribed species of Puccinia, viz., P. apdensia, P. decidua, P. dermatis, and P. lianchengensis, spp. nov. P. apdensia is characterized by its smooth teliospores with thickened apex. P. decidua represents the first Puccinia species inhabiting the host Anaphalis hancockii and is distinguished from the other Puccinia species by its telia and uredinia surrounded by the epidermis. P. dermatis from Halenia elliptica differs from the other Puccinia species on the host genus Halenia by the telia that have epidermis and teliospores with sparsely irregular granulated protrusions. P. lianchengensis is characterized by its teliospore surface with fishnet ornamentation and urediniospores without prominent caps. All of the new species are described and illustrated in this study.
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Affiliation(s)
- Chang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Yi-Fan Liu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Ying-Mei Liang
- Museum of Beijing Forestry University, Beijing Forestry University, Beijing 100083, China
| | - Lei Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Beijing Museum of Natural History, Beijing 100050, China
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Bawane P, Deshpande S, Yele S. Industrial and Pharmaceutical Applications of Microbial Diversity of Hypersaline Ecology from Lonar Soda Crater. Curr Pharm Biotechnol 2024; 25:1564-1584. [PMID: 38258768 DOI: 10.2174/0113892010265978231109085224] [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: 07/30/2023] [Revised: 09/16/2023] [Accepted: 10/04/2023] [Indexed: 01/24/2024]
Abstract
The unidentified geochemical and physiochemical characteristics of Soda Lakes across the globe make it a novel reservoir and bring attention to scientific civic for its conceivable industrial and pharmaceutical applications. In India, in the Maharashtra state, Lonar Lake is a naturally created Soda Lake by a meteorite impact. Phylogenetic data from this lake explored a diverse array of microorganisms like haloalkaliphilic bacteria and Archaea. Previously reported studies postulated the major microbial communities present in this lake ecosystem are Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria. Furthermore, it also contains Bacteroidetes, Nitrospirae, and Verrucomicrobia. This lake is also rich in phytoplankton, with the predominant presence of the Spirulina plantensis. Unique microbial strains from Lonar Lake ecosystems have fascinated consideration as a source of biological molecules with medicinal, industrial, and biotechnological potential. Recent literature revealed the isolation of antibioticproducing bacteria and alkaline proteases-producing alkaliphilic bacterium, as well as novel species of rare methylotrophs, other bacterial strains involved in producing vital enzymes, and unique actinomycetes are also reported. It indicates that the novel bacterial assemblage not reached hitherto may exist in this modified and unique ecology. This comprehensive review provides information about microbial diversity and its industrial and pharmaceutical interests that exist in Lonar Lake, which could be the future source of bioactive enzymes, biosurfactants, and biofuel and also useful in bioremediation. Furthermore, the novel species of microorganisms isolated from Lonar Lake have applications in the biosynthesis of medicines like antibiotics, antivirals, antifungals, anti-inflammatory agents, and precursors for synthesising valuable products. Data consolidated in the present review will cater to the needs of emerging industrial sectors for their commercial and therapeutic applications.
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Affiliation(s)
- Pradip Bawane
- Department of Pharmacognosy, SVKM's NMIMS, Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, Mumbai, 400056, India
- Department of Pharmacognosy, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, Maharashtra, India
| | - Shirish Deshpande
- Department of Pharmaceutical Chemistry, SVKM's NMIMS, School of Pharmacy & Technology Management, Telangana Hyderabad, 509301, India
| | - Santosh Yele
- Department of Pharmacognosy, SVKM's NMIMS, School of Pharmacy & Technology Management, Telangana Hyderabad, 509301, India
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Smith NEC. Call me by your name: Considerations of DNA sequences as types within wider discussions on fungal nomenclature. Mycology 2023; 15:137-143. [PMID: 38813474 PMCID: PMC11132796 DOI: 10.1080/21501203.2023.2295412] [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: 09/20/2023] [Accepted: 12/11/2023] [Indexed: 05/31/2024] Open
Abstract
This paper discusses the interaction between two substantial debates in taxonomy and nomenclature: The potential introduction of DNA-only types into fungal taxonomy and whether certain species names are offensive and should be changed. It argues that the acceptance of DNA sequences as types will likely lead to a proliferation of eponyms (species named after a person or persons) and that this will render them more likely to censure thus creating a point of instability in the fungal nomenclature. More fundamentally, it seeks to highlight the cultural and aesthetic attraction of names and to promote wider conversation on why we consider the Latin binomial central in our description of species.
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Pereira DS, Phillips AJL. Palm Fungi and Their Key Role in Biodiversity Surveys: A Review. J Fungi (Basel) 2023; 9:1121. [PMID: 37998926 PMCID: PMC10672035 DOI: 10.3390/jof9111121] [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: 10/15/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
Over the past three decades, a wealth of studies has shown that palm trees (Arecaceae) are a diverse habitat with intense fungal colonisation, making them an important substratum to explore fungal diversity. Palm trees are perennial, monocotyledonous plants mainly restricted to the tropics that include economically important crops and highly valued ornamental plants worldwide. The extensive research conducted in Southeast Asia and Australasia indicates that palm fungi are undoubtedly a taxonomically diverse assemblage from which a remarkable number of new species is continuously being reported. Despite this wealth of data, no recent comprehensive review on palm fungi exists to date. In this regard, we present here a historical account and discussion of the research on the palm fungi to reflect on their importance as a diverse and understudied assemblage. The taxonomic structure of palm fungi is also outlined, along with comments on the need for further studies to place them within modern DNA sequence-based classifications. Palm trees can be considered model plants for studying fungal biodiversity and, therefore, the key role of palm fungi in biodiversity surveys is discussed. The close association and intrinsic relationship between palm hosts and palm fungi, coupled with a high fungal diversity, suggest that the diversity of palm fungi is still far from being fully understood. The figures suggested in the literature for the diversity of palm fungi have been revisited and updated here. As a result, it is estimated that there are about 76,000 species of palm fungi worldwide, of which more than 2500 are currently known. This review emphasises that research on palm fungi may provide answers to a number of current fungal biodiversity challenges.
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Affiliation(s)
- Diana S. Pereira
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Alan J. L. Phillips
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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Pereira DS, Hilário S, Gonçalves MFM, Phillips AJL. Diaporthe Species on Palms: Molecular Re-Assessment and Species Boundaries Delimitation in the D. arecae Species Complex. Microorganisms 2023; 11:2717. [PMID: 38004729 PMCID: PMC10673533 DOI: 10.3390/microorganisms11112717] [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: 09/28/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Due to cryptic diversification, phenotypic plasticity and host associations, multilocus phylogenetic analyses have become the most important tool in accurately identifying and circumscribing species in the Diaporthe genus. However, the application of the genealogical concordance criterion has often been overlooked, ultimately leading to an exponential increase in novel Diaporthe spp. Due to the large number of species, many lineages remain poorly understood under the so-called species complexes. For this reason, a robust delimitation of the species boundaries in Diaporthe is still an ongoing challenge. Therefore, the present study aimed to resolve the species boundaries of the Diaporthe arecae species complex (DASC) by implementing an integrative taxonomic approach. The Genealogical Phylogenetic Species Recognition (GCPSR) principle revealed incongruences between the individual gene genealogies. Moreover, the Poisson Tree Processes' (PTPs) coalescent-based species delimitation models identified three well-delimited subclades represented by the species D. arecae, D. chiangmaiensis and D. smilacicola. These results evidence that all species previously described in the D. arecae subclade are conspecific, which is coherent with the morphological indistinctiveness observed and the absence of reproductive isolation and barriers to gene flow. Thus, 52 Diaporthe spp. are reduced to synonymy under D. arecae. Recent population expansion and the possibility of incomplete lineage sorting suggested that the D. arecae subclade may be considered as ongoing evolving lineages under active divergence and speciation. Hence, the genetic diversity and intraspecific variability of D. arecae in the context of current global climate change and the role of D. arecae as a pathogen on palm trees and other hosts are also discussed. This study illustrates that species in Diaporthe are highly overestimated, and highlights the relevance of applying an integrative taxonomic approach to accurately circumscribe the species boundaries in the genus Diaporthe.
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Affiliation(s)
- Diana S. Pereira
- Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal;
| | - Sandra Hilário
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Porto, Portugal;
- Faculty of Sciences, Biology Department, University of Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Micael F. M. Gonçalves
- Faculty of Sciences, Biology Department, University of Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
- Centre for Environmental and Marine Studies, Department of Biology, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Alan J. L. Phillips
- Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal;
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Duong TKC, Tran VL, Nguyen TB, Nguyen TT, Ho NTK, Nguyen TQ. Ensemble learning-based approach for automatic classification of termite mushrooms. Front Genet 2023; 14:1208695. [PMID: 37886685 PMCID: PMC10598762 DOI: 10.3389/fgene.2023.1208695] [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: 04/19/2023] [Accepted: 09/13/2023] [Indexed: 10/28/2023] Open
Abstract
Termite mushrooms are edible fungi that provide significant economic, nutritional, and medicinal value. However, identifying these mushroom species based on morphology and traditional knowledge is ineffective due to their short development time and seasonal nature. This study proposes a novel method for classifying termite mushroom species. The method utilizes Gradient Boosting machine learning techniques and sequence encoding on the Internal Transcribed Spacer (ITS) gene dataset to construct a machine learning model for identifying termite mushroom species. The model is trained using ITS sequences obtained from the National Center for Biotechnology Information (NCBI) and the Barcode of Life Data Systems (BOLD). Ensemble learning techniques are applied to classify termite mushroom species. The proposed model achieves good results on the test dataset, with an accuracy of 0.91 and an average AUCROC value of 0.99. To validate the model, eight ITS sequences collected from termite mushroom samples in An Linh commune, Phu Giao district, Binh Duong province, Vietnam were used as the test data. The results show consistent species identification with predictions from the NCBI BLAST software. The results of species identification were consistent with the NCBI BLAST prediction software. This machine-learning model shows promise as an automatic solution for classifying termite mushroom species. It can help researchers better understand the local growth of these termite mushrooms and develop conservation plans for this rare and valuable plant resource.
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Affiliation(s)
- Thi Kim Chi Duong
- Department of Information Technology, Lac Hong University, Dong Nai Province, Vietnam
- Faculty of Engineering and Technology, Thu Dau Mot University, Binh Duong Province, Vietnam
| | - Van Lang Tran
- HUFLIT Journal of Science, Ho Chi Minh City University of Foreign Languages and Information Technology, Ho Chi Minh City, Vietnam
| | - The Bao Nguyen
- Faculty of Engineering and Technology, Thu Dau Mot University, Binh Duong Province, Vietnam
| | - Thi Thuy Nguyen
- Faculty of Engineering and Technology, Thu Dau Mot University, Binh Duong Province, Vietnam
| | - Ngoc Trung Kien Ho
- Faculty of Engineering and Technology, Thu Dau Mot University, Binh Duong Province, Vietnam
| | - Thanh Q. Nguyen
- Department of Railway-Metro Engineering, Ho Chi Minh City University of Transport, Ho Chi Minh City, Vietnam
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Fungal Diversity in Korean Caves and Cave-Inhabiting Bats with Attention to Pseudogymnoascus Species. DIVERSITY 2023. [DOI: 10.3390/d15020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Pseudogymnoascus is a psychrophilic fungus, which is a genus widely distributed in cold regions around the world. Recently, the presence of Pseudogymnoascus destructans (Pd), the causative agent of white-nose syndrome (WNS) belonging to Pseudogymnoascus, has been reported in neighboring countries of Korea. However, no investigation on Pd has been reported in Korea. In this study, cave-inhabiting bats and their habitats were investigated in terms of the diversity of cave fungi, and we tried to confirm the presence of Pd. Three caves suspected of hosting Pd were selected, and 83 environmental and 53 bat samples were collected. A total of 154 fungal strains belonging to 31 different genera were isolated, and 20 of 154 were confirmed to belong to Pseudogymnoascus. Pd-diagnostic PCR was performed to check whether Pd was present in the isolated Pseudogymnoascus, and seven positives were confirmed. However, phylogenetic analyses revealed that no isolates belonged or were closely related to the clade with Pd. Although samples were collected from limited areas, undescribed Pseudogymnoascus species were isolated, and it was confirmed that Korean isolates were distributed in various clades. In conclusion, it is hypothesized that Korean Pseudogymnoascus presents high diversity.
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Pushparaj K, Meyyazhagan A, Bhotla HK, Arumugam VA, Pappuswamy M, Vadivalagan C, Hakeem KR, Balasubramanian B, Liu W, Mousavi Khaneghah A. The crux of bioactive metabolites in endophytic and thermophilic fungi and their proximal prospects in biotechnological and industrial domains. Toxicon 2023; 223:107007. [PMID: 36563862 DOI: 10.1016/j.toxicon.2022.107007] [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: 10/25/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Fungi are ubiquitous in distribution and are found in grasses to hot springs. Their mode of nutrition provides sustenance for living and propagation. Ironically, varied fungal species have developed customized strategies for protection and survival by producing diverse secondary metabolites. The review aimed to project the contrasting potential features of the endophytic and thermophilic fungi groups. The metabolites and the enzymes of endophytic and thermophilic fungi served as the backbone to thrive and adapt within-host and in extreme conditions like higher pH, heat, and salinity, respectively. Identification, knowledge of their biochemistry and pathway, exploration, production, and utilization of these bioactive molecules in various commercial, industrial, and pharmaceutical domains were briefly discussed. The uniqueness of endophytes includes stress management and improved biomass production of the host, green fuel production, omnipresence, selected triple-symbiosis with the virus, synthesis of polyketides, and other active metabolites are widely used in biomedical applications and agriculture management. This review attempted to limelight the specific applications of thermophilic fungal metabolites and the roles of thermo-stable enzymes in bioprospecting. Moreover, probing the metabolites of thermophiles rendered novel antibiotic compounds, which were proven effective against multi-drug resistant bacteria and harboured the potential to curtail infectious diseases.
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Affiliation(s)
- Karthika Pushparaj
- Department of Zoology, School of Biosciences, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641 043, Tamil Nadu, India
| | - Arun Meyyazhagan
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | - Haripriya Kuchi Bhotla
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | - Vijaya Anand Arumugam
- Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, 641 046, Tamil Nadu, India
| | - Manikantan Pappuswamy
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | | | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
| | | | - Wenchao Liu
- Department of Animal Science, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China.
| | - Amin Mousavi Khaneghah
- Department of Fruit and Vegetable Product Technology, Prof. WacławDąbrowski Institute of Agricultural and Food Biotechnology - State Research Institute, 36 Rakowiecka St., 02-532, Warsaw, Poland; Department of Technology of Chemistry, Azerbaijan State Oil and Industry University, Baku, Azerbaijan.
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Olou B, Langer E, Ryvarden L, Krah FS, Hounwanou G, Piepenbring M, Yorou N. New records and barcode sequence data of wood-inhabiting polypores in Benin with notes on their phylogenetic placements and distribution. Fungal Syst Evol 2023; 11:11-42. [PMID: 37469936 PMCID: PMC10353294 DOI: 10.3114/fuse.2023.11.02] [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: 08/16/2022] [Accepted: 01/13/2023] [Indexed: 07/21/2023] Open
Abstract
Wood-inhabiting fungi (WIF), such as polypores, are extremely species-rich and play vital roles in the functioning of forest ecosystems as decomposers. Despite the importance of polypores, our knowledge of the diversity and distribution of these fungi is still poor in general and especially for West Africa. To advance our knowledge we here summarise results from field collections between 2017 and 2021 and present (i) a taxonomic overview, (ii) phylogenetic placements and (iii) an illustrated catalogue of wood-inhabiting polypore fungi with colour pictures. During the field sampling campaigns, we collected 647 specimens. Based on morphological characteristics and molecular barcode data, 76 polypore species belonging to six orders, 15 families and 39 genera were identified. Of the 76 species, 30 are new to the West Africa, 69 new to Benin, and two new combinations Fuscoporia beninensis and Megasporia minuta are proposed. With this summary, we provide new data for further research. Citation: Olou BA, Langer E, Ryvarden L, Krah F-S, Hounwanou GB, Piepenbring M, Yorou NS (2023). New records and barcode sequence data of wood-inhabiting polypores in Benin with notes on their phylogenetic placements and distribution. Fungal Systematics and Evolution 11: 11-42. doi: 10.3114/fuse.2023.11.02.
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Affiliation(s)
- B.A. Olou
- Research Unit Tropical Mycology and Plants-Soil Fungi Interactions (MyTIPS), Faculty of Agronomy, University of Parakou, BP 123 Parakou, Benin
| | - E. Langer
- Department of Ecology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, Germany
| | - L. Ryvarden
- Institute of Biology, University of Oslo, P.O. Box 1066, Blindern, N-0316 Oslo, Norway
| | - F.-S. Krah
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Conservation Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - G.B. Hounwanou
- Research Unit Tropical Mycology and Plants-Soil Fungi Interactions (MyTIPS), Faculty of Agronomy, University of Parakou, BP 123 Parakou, Benin
| | - M. Piepenbring
- Department of Mycology, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - N.S. Yorou
- Research Unit Tropical Mycology and Plants-Soil Fungi Interactions (MyTIPS), Faculty of Agronomy, University of Parakou, BP 123 Parakou, Benin
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Wijayawardene NN, Dai DQ, Jayasinghe PK, Gunasekara SS, Nagano Y, Tibpromma S, Suwannarach N, Boonyuen N. Ecological and Oceanographic Perspectives in Future Marine Fungal Taxonomy. J Fungi (Basel) 2022; 8:1141. [PMID: 36354908 PMCID: PMC9696965 DOI: 10.3390/jof8111141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2023] Open
Abstract
Marine fungi are an ecological rather than a taxonomic group that has been widely researched. Significant progress has been made in documenting their phylogeny, biodiversity, ultrastructure, ecology, physiology, and capacity for degradation of lignocellulosic compounds. This review (concept paper) summarizes the current knowledge of marine fungal diversity and provides an integrated and comprehensive view of their ecological roles in the world's oceans. Novel terms for 'semi marine fungi' and 'marine fungi' are proposed based on the existence of fungi in various oceanic environments. The major maritime currents and upwelling that affect species diversity are discussed. This paper also forecasts under-explored regions with a greater diversity of marine taxa based on oceanic currents. The prospects for marine and semi-marine mycology are highlighted, notably, technological developments in culture-independent sequencing approaches for strengthening our present understanding of marine fungi's ecological roles.
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Affiliation(s)
- Nalin N. Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Section of Genetics, Institute for Research and Development in Health and Social Care, No: 393/3, Lily Avenue, Off Robert Gunawardane Mawatha, Battaramulla 10120, Sri Lanka
- National Institute of Fundamental Studies, Hantana Road, Kandy 20000, Sri Lanka
| | - Don-Qin Dai
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Prabath K. Jayasinghe
- National Aquatic Resources Research and Development Agency (NARA), Crow Island, Colombo 00150, Sri Lanka
| | - Sudheera S. Gunasekara
- National Aquatic Resources Research and Development Agency (NARA), Crow Island, Colombo 00150, Sri Lanka
| | - Yuriko Nagano
- Deep-Sea Biodiversity Research Group, Marine Biodiversity and Environmental Assessment Research Center, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Saowaluck Tibpromma
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nattawut Boonyuen
- Plant Microbe Interaction Research Team (APMT), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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Chaithra M, Prameeladevi T, Bhagyasree SN, Prasad L, Subramanian S, Kamil D. “Multilocus sequence analysis for population diversity of indigenous entomopathogenic fungus Beauveria bassiana and its bio-efficacy against the cassava mite, Tetranychus truncatus Ehara (Acari: Tetranychidae)”. Front Microbiol 2022; 13:1007017. [PMID: 36304955 PMCID: PMC9593087 DOI: 10.3389/fmicb.2022.1007017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/13/2022] [Indexed: 11/14/2022] Open
Abstract
Beauveria bassiana is an entomopathogenic fungus that causes the white muscadine disease in insects. The majority of entomopathogenic fungi are soil and insect borne, 15 soil samples were collected from seven different locations during 2021, from January to December. Similarly, during 2022, March to December, 15 fungus-infected insect specimens were collected from five different locations hence soil and insect samples from various ecosystems were collected. As a result, 30 B. bassiana isolates from 11 different geographical areas were identified using morphological characteristics and multilocus sequence data in this investigation. The taxonomical positions of the isolates were determined using morphological characteristics and phylogenetic inferences based on three loci (Internal Transcribed Sequence, Elongation Factor-1α, and B. bassiana chitinase 1). In phylogenetic analysis of B. bassiana, the Maximum Likelihood analytical method produced distinct tree topology when compared to Neighbor-joining and minimum evolution. Three isolates viz., Bb3, Bb7 and Bb20 were found closely linked with reference isolate (KTU-24) and other showed the higher population diversity among them. The genetic distances of 30 B. bassiana isolates revealed that 15 were not closely related (D varied from 0.003 to 0.036). The pathogenicity of B. bassiana isolates from various hosts along with one commercial formulation (Beveroz) was assessed against Tetranychus truncatus under in vitro conditions by a completely randomized design (CRD) experiment. The same experiment was repeated thrice to confirm the pathogenicity of B. bassiana against T. truncatus. Later, the collected T. truncatus mortality data was converted into corrected mortality by using the Abbott formula and the values were examined using analysis of variance (ANOVA) in SPSS 23.0 software. Duncan’s Multiple Comparison Test was also done to compare the percentage mortality rates among the 30 B. bassiana isolates. The recorded results showed that the Bb6, Bb15 and Bb12 isolates caused significantly higher mortality of T. truncatus, i.e., 97.73, 96.73 and 94.50% respectively, than the other isolates. This study showed the relativeness among the B. bassiana isolates and establishes their bio-efficacy against T. truncatus, which further can be used for commercialization as bio-pesticide.
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Affiliation(s)
- M. Chaithra
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - T. Prameeladevi
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S. N. Bhagyasree
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - L. Prasad
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S. Subramanian
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Deeba Kamil
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Deeba Kamil,
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Nganga EM, Kyallo M, Orwa P, Rotich F, Gichuhi E, Kimani JM, Mwongera D, Waweru B, Sikuku P, Musyimi DM, Mutiga SK, Ziyomo C, Murori R, Wasilwa L, Correll JC, Talbot NJ. Foliar Diseases and the Associated Fungi in Rice Cultivated in Kenya. PLANTS 2022; 11:plants11091264. [PMID: 35567265 PMCID: PMC9105481 DOI: 10.3390/plants11091264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022]
Abstract
We conducted a survey to assess the occurrence and severity of rice blast and brown spot diseases on popular cultivars grown in the Busia, Kirinyaga, and Kisumu counties of Kenya in 2019. Working with agricultural extension workers within rice production areas, we interviewed farmers (n = 89) regarding their preferred cultivars and their awareness of blast disease, as this was the major focus of our research. We scored the symptoms of blast and brown spot and assessed the lodging, plant height, and maturity of the crops (days after planting). Furthermore, we collected leaf and neck tissues for the assessment of the prevailing fungal populations. We used specific DNA primers to screen for the prevalence of the causal pathogens of blast, Magnaporthe oryzae, and brown spot, Cochliobolus miyabeanus, on asymptomatic and symptomatic leaf samples. We also conducted fungal isolations and PCR-sequencing to identify the fungal species in these tissues. Busia and Kisumu had a higher diversity of cultivars compared to Kirinyaga. The aromatic Pishori (NIBAM 11) was preferred and widely grown for commercial purposes in Kirinyaga, where 86% of Kenyan rice is produced. NIBAM108 (IR2793-80-1) and BW196 (NIBAM 109) were moderately resistant to blast, while NIBAM110 (ITA310) and Vietnam were susceptible. All the cultivars were susceptible to brown spot except for KEH10005 (Arize Tej Gold), a commercial hybrid cultivar. We also identified diverse pathogenic and non-pathogenic fungi, with a high incidence of Nigrospora oryzae, in the rice fields of Kirinyaga. There was a marginal correlation between disease severity/incidence and the occurrence of causal pathogens. This study provides evidence of the need to strengthen pathogen surveillance through retraining agricultural extension agents and to breed for blast and brown spot resistance in popular rice cultivars in Kenya.
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Affiliation(s)
- Everlyne M. Nganga
- Department of Botany, School of Physical and Biological Sciences, Maseno University, Kisumu P.O. Box 3275-40100, Kenya; (E.M.N.); (P.S.); (D.M.M.)
| | - Martina Kyallo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
| | - Philemon Orwa
- Department of Water and Agricultural Resource Management, School of Agriculture, University of Embu, Embu P.O. Box 6-60100, Kenya; (P.O.); (F.R.)
| | - Felix Rotich
- Department of Water and Agricultural Resource Management, School of Agriculture, University of Embu, Embu P.O. Box 6-60100, Kenya; (P.O.); (F.R.)
| | - Emily Gichuhi
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - John M. Kimani
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - David Mwongera
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - Bernice Waweru
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
| | - Phoebe Sikuku
- Department of Botany, School of Physical and Biological Sciences, Maseno University, Kisumu P.O. Box 3275-40100, Kenya; (E.M.N.); (P.S.); (D.M.M.)
| | - David M. Musyimi
- Department of Botany, School of Physical and Biological Sciences, Maseno University, Kisumu P.O. Box 3275-40100, Kenya; (E.M.N.); (P.S.); (D.M.M.)
| | - Samuel K. Mutiga
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
- Eastern and Southern Region Office, International Rice Research Institute, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya;
- Correspondence:
| | - Cathrine Ziyomo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
| | - Rosemary Murori
- Department of Entomology and Plant Pathology, Division of Agriculture, The University of Arkansas System, Fayetteville, AR 72701, USA;
| | - Lusike Wasilwa
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - James C. Correll
- Eastern and Southern Region Office, International Rice Research Institute, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya;
| | - Nicholas J. Talbot
- The Sainsbury Laboratory, Norwich Research Park, University of East Anglia, Norwich NR4 7UH, UK;
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Quijada L, Matočec N, Kušan I, Tanney JB, Johnston PR, Mešić A, Pfister DH. Apothecial Ancestry, Evolution, and Re-Evolution in Thelebolales (Leotiomycetes, Fungi). BIOLOGY 2022; 11:biology11040583. [PMID: 35453781 PMCID: PMC9026407 DOI: 10.3390/biology11040583] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022]
Abstract
Simple Summary Leotiomycetes is one of the most speciose classes of the phylum Ascomycota (Fungi). Its species are mainly apothecioid, paraphysate, and possess active ascospore discharge. Thelebolales are a distinctive order of the Leotiomycetes class whose members have mostly closed ascomata, evanescent asci, and thus passively dispersed ascospores. Within the order, a great diversity of peridia have evolved as adaptations to different dispersal strategies. The genus Thelebolus is an exceptional case of ascomatal evolution within the order. Its species are the most diverse in functional traits, encompassing species with closed ascomata and evanescent asci, and species with open ascomata, active ascospore discharge, and paraphyses. Open ascomata were previously suggested as the ancestral state in the genus, these ascomata depend on mammals and birds as dispersal agents. In our work, we used morphological and phylogenetic methods, as well as the reconstruction of ancestral traits for ascomatal type, asci dehiscence, the presence or absence of paraphyses, and ascospore features to explore evolution within Thelebolales. We demonstrate the apothecial ancestry in Thelebolales and propose a new hypothesis about the evolution of the open ascomata in Thelebolus involving a process of re-evolution where the active dispersal of ascospores appears independently twice within the order. A new family, Holwayaceae, is proposed within Thelebolales, comprising three genera: Holwaya, Patinella, and Ramgea. Abstract Closed cleistothecia-like ascomata have repeatedly evolved in non-related perithecioid and apothecioid lineages of lichenized and non-lichenized Ascomycota. The evolution of a closed, darkly pigmented ascoma that protects asci and ascospores is conceived as either an adaptation to harsh environmental conditions or a specialized dispersal strategy. Species with closed ascomata have mostly lost sterile hymenial elements (paraphyses) and the capacity to actively discharge ascospores. The class Leotiomycetes, one of the most speciose classes of Ascomycota, is mainly apothecioid, paraphysate, and possesses active ascospore discharge. Lineages with closed ascomata, and their morphological variants, have evolved independently in several families, such as Erysiphaceae, Myxotrichaceae, Rutstroemiaceae, etc. Thelebolales is a distinctive order in the Leotiomycetes class. It has two widespread families (Thelebolaceae, Pseudeurotiaceae) with mostly closed ascomata, evanescent asci, and thus passively dispersed ascospores. Within the order, closed ascomata dominate and a great diversity of peridia have evolved as adaptations to different dispersal strategies. The type genus, Thelebolus, is an exceptional case of ascomatal evolution within the order. Its species are the most diverse in functional traits, encompassing species with closed ascomata and evanescent asci, and species with open ascomata, active ascospore discharge, and paraphyses. Open ascomata were previously suggested as the ancestral state in the genus, these ascomata depend on mammals and birds as dispersal agents. In this scheme, species with closed ascomata, a lack of paraphyses, and passive ascospore discharge exhibit derived traits that evolved in adaptation to cold ecosystems. Here, we used morphological and phylogenetic methods, as well as the reconstruction of ancestral traits for ascomatal type, asci dehiscence, the presence or absence of paraphyses, and ascospore features to explore evolution within Thelebolales. We demonstrate the apothecial ancestry in Thelebolales and propose a new hypothesis about the evolution of the open ascomata in Thelebolus, involving a process of re-evolution where the active dispersal of ascospores appears independently twice within the order. We propose a new family, Holwayaceae, within Thelebolales, that retains the phenotypic features exhibited by species of Thelebolus, i.e., pigmented capitate paraphyses and active asci discharge with an opening limitation ring.
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Affiliation(s)
- Luis Quijada
- Department of Organismic and Evolutionary Biology, The Farlow Reference Library and Herbarium of Cryptogamic Botany, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA;
- Correspondence: (L.Q.); (I.K.)
| | - Neven Matočec
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia; (N.M.); (A.M.)
| | - Ivana Kušan
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia; (N.M.); (A.M.)
- Correspondence: (L.Q.); (I.K.)
| | - Joey B. Tanney
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 Burnside Road, Victoria, BC V8Z 1M5, Canada;
| | - Peter R. Johnston
- Manaaki Whenua Landcare Research, Private Bag 92170, Auckland 1072, New Zealand;
| | - Armin Mešić
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia; (N.M.); (A.M.)
| | - Donald H. Pfister
- Department of Organismic and Evolutionary Biology, The Farlow Reference Library and Herbarium of Cryptogamic Botany, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA;
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15
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Cazabonne J, Bartrop L, Dierickx G, Gafforov Y, Hofmann TA, Martin TE, Piepenbring M, Rivas-Ferreiro M, Haelewaters D. Molecular-Based Diversity Studies and Field Surveys Are Not Mutually Exclusive: On the Importance of Integrated Methodologies in Mycological Research. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:860777. [PMID: 37746218 PMCID: PMC10512293 DOI: 10.3389/ffunb.2022.860777] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 02/21/2022] [Indexed: 09/26/2023]
Abstract
Understanding and describing the diversity of living organisms is a great challenge. Fungi have for a long time been, and unfortunately still are, underestimated when it comes to taxonomic research. The foundations were laid by the first mycologists through field observations. These important fundamental works have been and remain vital reference works. Nevertheless, a non-negligible part of the studied funga escaped their attention. Thanks to modern developments in molecular techniques, the study of fungal diversity has been revolutionized in terms of tools and knowledge. Despite a number of disadvantages inherent to these techniques, traditional field-based inventory work has been increasingly superseded and neglected. This perspective aims to demonstrate the central importance of field-based research in fungal diversity studies, and encourages researchers not to be blinded by the sole use of molecular methods.
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Affiliation(s)
- Jonathan Cazabonne
- Groupe de Recherche en Écologie de la MRC Abitibi (GREMA), Institut de Recherche sur les Forêts (IRF), Université du Québec en Abitibi-Témiscamingue, Amos, QC, Canada
| | | | - Glen Dierickx
- Research Group Mycology, Department of Biology, Ghent University, Ghent, Belgium
- Research Institute for Nature and Forest (INBO), Brussels, Belgium
| | - Yusufjon Gafforov
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Tina A. Hofmann
- Centro de Investigaciones Micológicas (CIMi), Herbario UCH, Universidad Autónoma de Chiriquí, David, Panama
| | - Thomas E. Martin
- Operation Wallacea Ltd, Wallace House, Old Bolingbroke, United Kingdom
| | - Meike Piepenbring
- Mycology Working Group, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Mauro Rivas-Ferreiro
- Population Genetics and Cytogenetics Group, Facultade de Bioloxía, Universidade de Vigo, Vigo, Spain
| | - Danny Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, Ghent, Belgium
- Centro de Investigaciones Micológicas (CIMi), Herbario UCH, Universidad Autónoma de Chiriquí, David, Panama
- Operation Wallacea Ltd, Wallace House, Old Bolingbroke, United Kingdom
- Faculty of Science, University of South Bohemia, Ceské Budějovice, Czechia
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Fernandez-Triana JL. Turbo taxonomy approaches: lessons from the past and recommendations for the future based on the experience with Braconidae (Hymenoptera) parasitoid wasps. Zookeys 2022; 1087:199-220. [PMID: 35585942 PMCID: PMC8897373 DOI: 10.3897/zookeys.1087.76720] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/02/2022] [Indexed: 12/22/2022] Open
Abstract
Not aplicable to a Forum paper, but if needed I can write one.
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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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Hilário S, Santos L, Phillips AJL, Alves A. Caveats of the internal transcribed spacer region as a barcode to resolve species boundaries in Diaporthe. Fungal Biol 2021; 126:54-74. [PMID: 34930559 DOI: 10.1016/j.funbio.2021.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 07/13/2021] [Accepted: 10/25/2021] [Indexed: 01/03/2023]
Abstract
Species in Diaporthe are largely reported as important plant pathogens. Identification of species in this genus has been complemented by morphological and molecular features. However, one important factor delaying this process is the struggle to formulate robust species concepts to create adequate international phytosanitary measures. Regardless of the wide use of the internal transcribed spacer (ITS) rDNA region, established as the primary DNA barcode for fungi, the tendency for intraspecific variation has been reported, misleading interpretation of phylogenetic analyses. Therefore, the present study aimed to illustrate, using specific examples, how the ITS region may be problematic for species delimitation. We showed that the ITS region is highly variable, with strains of Diaporthe malorum and Diaporthe novem falling into more than one clade, which if analyzed on their own, would be likely recognized as distinct taxa. Divergent ITS paralogs were also proven to coexist within the genome of D. novem. We also suggest that ITS may have escaped from concerted evolution or has undergone a duplication event. Furthermore, this study reports for the first time the existence of a putative hybrid in the genus Diaporthe. Our findings offer new clues towards the intraspecific and intragenomic variation in the ITS region, raising questions about its value for barcoding, i.e., identifying species in the genus Diaporthe. Therefore, we recommend that the ITS region be analyzed cautiously and always compared for congruence prior to description of novel taxa.
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Affiliation(s)
- Sandra Hilário
- CESAM, Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Liliana Santos
- CESAM, Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Alan J L Phillips
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
| | - Artur Alves
- CESAM, Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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Ijaz M, Afza R, Zafar M, Hamayun M, Khan SM, Ahmad Z, Ahmad M, Khan SA, Shah R, Yahya M. Taxonomic investigation of selected rust fungi using scanning electron microscopy from Khyber Pakhtunkhwa, Pakistan. Microsc Res Tech 2021; 85:755-766. [PMID: 34570406 DOI: 10.1002/jemt.23947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
Rusts comprises the largest natural group of plant pathogens including approximately 8% of all described Fungi. Rust fungi are extremely plant pathogens responsible for great losses to agriculture productivity. Rust species belong to several genera among which more than half are Puccinia species. In Pakistan, rust causes severe damage to agriculture crops. Current study was carried out to identify and characterize different rust species common in the research area through microscopy and Scanning electron microscopy (SEM) in Khyber Pakhtunkhwa, Pakistan. Morpho-anatomical investigation of each collected rust species was carried out using different standard protocols. The dimensions of spores were measured and snapped under a stereomicroscope. SEM was used to examine the shape, size, and ornamentation of the spores of each rust fungus. Results revealed documentation of seven rust fungi, that is, Melampsora euphorbiae, Phragmidium barclayi, Puccinia nepalensis, P. exhausta, P. menthae, Uromyces capitatus, and Uromyces decorates belong to four different genera, were recorded. SEM revealed that spermogonia and Aecia were missing in most of the rust fungus studied. Uredinia was found in a scattered, irregular, lengthy, and epidermis-enclosed form. Urediniospores were found to be ovulating, elongated, echinulate, globose to sub-globose, ellipsoid to ovoid, and globose to sub-globose. Telia was found as sub-epidermal, amphigenous, dispersed, minute, and spherical cells. Teliospores ranged in form from cylindrical to oblong. The germ pores were detected in both apical (top cell) and basal (bottom cell) idiosyncratic and pedicel-attached cells. The techniques used in the current investigation will aid mycologists in rust identification and microscopic characterization.
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Affiliation(s)
- Murtaza Ijaz
- Department of Botany, Hazara University Mansehra, Mansehra, Pakistan
| | - Rabia Afza
- Department of Botany, Hazara University Mansehra, Mansehra, Pakistan
| | - Muhammad Zafar
- Department of Plant Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Muhammad Hamayun
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
| | - Shujaul Mullk Khan
- Department of Plant Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Zeeshan Ahmad
- Department of Plant Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Mushtaq Ahmad
- Department of Plant Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Sumera Afzal Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Raheem Shah
- Department of Botany, Hazara University Mansehra, Mansehra, Pakistan
| | - Muhammad Yahya
- Department of Botany, Hazara University Mansehra, Mansehra, Pakistan
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21
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Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa. J Fungi (Basel) 2021; 7:jof7090703. [PMID: 34575741 PMCID: PMC8467358 DOI: 10.3390/jof7090703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 01/08/2023] Open
Abstract
Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual-asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.
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Gao T, Liu Y, Liu X, Zhao K, Shan L, Wu Q, Liu Y, Zhang Z, Ma F, Li C. Exogenous dopamine and overexpression of the dopamine synthase gene MdTYDC alleviated apple replant disease. TREE PHYSIOLOGY 2021; 41:1524-1541. [PMID: 33171491 DOI: 10.1093/treephys/tpaa154] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/08/2020] [Indexed: 05/25/2023]
Abstract
Apple replant disease (ARD) is a soil-borne disease that leads to economic losses due to reduced plant growth and diminished fruit yields. Dopamine is involved in interactions between plants and pathogens. However, it remains unclear whether dopamine can directly stimulate defense responses to ARD. In this study, an exogenous dopamine treatment and dopamine synthetase MdTYDC (tyrosine decarboxylase) transgenic plants were used to verify the role of dopamine in treating ARD. First, 2-year-old apple trees (Malus domestica cv. Fuji), grafted onto rootstock M26, were grown in replant soils. The addition of dopamine (100 μM) to the soil promoted seedling growth and changed the accumulation of mineral elements in plants in replant soils. Such supplementation improved the activity of invertase, urease, proteinase and phosphatase under replant conditions. Sequencing analysis of 16S rDNA and internal transcribed spacer (ITS) rDNA revealed that dopamine had a slight influence on bacterial diversity but had an obvious effect on the fungal diversity in replant soils. The application of dopamine to replant soil changed the composition of bacterial and fungal communities. Second, overexpression of MdTYDC in apple plants alleviated the effects of ARD. MdTYDC transgenic lines exhibited mitigated ARD through inhibited degradation of photosynthetic pigment, maintaining the stability of photosystems I and II and improving the antioxidant system. Furthermore, overexpression of MdTYDC improved arbuscular mycorrhizal fungi colonization by improving the accumulation of soluble sugars under replant conditions. Together, these results demonstrated that dopamine enhances the tolerance of apples to ARD.
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Affiliation(s)
- Tengteng Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yusong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaomin Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kai Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qian Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhijun Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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De Lange R, Adamčík S, Adamčíkova K, Asselman P, Borovička J, Delgat L, Hampe F, Verbeken A. Enlightening the black and white: species delimitation and UNITE species hypothesis testing in the Russula albonigra species complex. IMA Fungus 2021; 12:20. [PMID: 34334127 PMCID: PMC8327428 DOI: 10.1186/s43008-021-00064-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/12/2021] [Indexed: 11/10/2022] Open
Abstract
Russula albonigra is considered a well-known species, morphologically delimited by the context of the basidiomata blackening without intermediate reddening, and the menthol-cooling taste of the lamellae. It is supposed to have a broad ecological range and a large distribution area. A thorough molecular analysis based on four nuclear markers (ITS, LSU, RPB2 and TEF1-α) shows this traditional concept of R. albonigra s. lat. represents a species complex consisting of at least five European, three North American, and one Chinese species. Morphological study shows traditional characters used to delimit R. albonigra are not always reliable. Therefore, a new delimitation of the R. albonigra complex is proposed and a key to the described European species of R. subgen. Compactae is presented. A lectotype and an epitype are designated for R. albonigra and three new European species are described: R. ambusta, R. nigrifacta, and R. ustulata. Different thresholds of UNITE species hypotheses were tested against the taxonomic data. The distance threshold of 0.5% gives a perfect match to the phylogenetically defined species within the R. albonigra complex. Publicly available sequence data can contribute to species delimitation and increase our knowledge on ecology and distribution, but the pitfalls are short and low quality sequences.
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Affiliation(s)
- Ruben De Lange
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Slavomír Adamčík
- Institute of Botany, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovakia
| | - Katarína Adamčíkova
- Institute of Forest Ecology Slovak Academy of Sciences, Akademická 2, 949 01, Nitra, Slovakia
| | - Pieter Asselman
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Jan Borovička
- Institute of Geology of the Czech Academy of Sciences, Rozvojová 269, 165 00, Prague 6, Czech Republic.,Nuclear Physics Institute of the Czech Academy of Sciences, Hlavní 130, 250 68, Husinec-Řež, Czech Republic
| | - Lynn Delgat
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.,Meise Botanic Garden, Research Department, Nieuwelaan 38, 1860, Meise, Belgium
| | - Felix Hampe
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Annemieke Verbeken
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
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Solving a long-standing enigma: Myrmicinosporidium durum belongs to Blastocladiomycota, a phylum of primarily aquatic fungi. J Invertebr Pathol 2021; 184:107640. [PMID: 34166714 DOI: 10.1016/j.jip.2021.107640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/05/2021] [Accepted: 06/13/2021] [Indexed: 11/22/2022]
Abstract
Myrmicinosporidium durumHölldobler (1933) is a widely distributed fungal endoparasite of ants. However, little is known about its biology, ecology, or evolutionary history. Our study investigated the phylogenetics of this entomopathogenic fungus using a molecular approach. Samples of M. durum were obtained from infected Solenopsis fugax workers collected in Warsaw (Poland). Analyses of rDNA markers revealed that M. durum belongs to a phylum of primarily aquatic fungi, Blastocladiomycota. It is currently the only species from this group known to parasitise hymenopterans. Our findings have clarified this fungus' taxonomy and suggest future directions for research into its biology, ecology, and infection dynamics.
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Narayanan A, Ismert KJ, Smith MD, Jumpponen A. Soil fungal communities are compositionally resistant to drought manipulations – Evidence from culture-dependent and culture-independent analyses. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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New insights into the systematics of Bactrodesmium and its allies and introducing new genera, species and morphological patterns in the Pleurotheciales and Savoryellales ( Sordariomycetes). Stud Mycol 2020; 95:415-466. [PMID: 32855744 PMCID: PMC7426232 DOI: 10.1016/j.simyco.2020.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The newly discovered systematic placement of Bactrodesmium abruptum, the lectotype species of the genus, prompted a re-evaluation of the traditionally broadly conceived genus Bactrodesmium. Fresh material, axenic cultures and new DNA sequence data of five gene regions of six species, i.e. B. abruptum, B. diversum, B. leptopus, B. obovatum, B. pallidum and B. spilomeum, were studied. Bactrodesmium is a strongly resolved lineage in the Savoryellales (Sordariomycetes), supported by Bayesian and Maximum Likelihood methods. The genus Bactrodesmium is emended and delimited to hyphomycetes characterised by sporodochial conidiomata, mononematous often fasciculate conidiophores, holoblastic conidiogenesis and acrogenous, solitary, dry, pigmented, transversely or rarely longitudinally septate conidia. The conidia are seceding rhexolytically, exhibiting multiple secession patterns. An identification key to 35 species accepted in Bactrodesmium is given, providing the most important diagnostic characters. Novel DNA sequence data of B. longisporum and B. stilboideum confirmed their placement in the Sclerococcales (Eurotiomycetes). For other Bactrodesmium, molecular data are available for B. cubense and B. gabretae, which position them in the Dothideomycetes and Leotiomycetes, respectively. All four species are excluded from Bactrodesmium and segregated into new genera, Aphanodesmium, Gamsomyces and Kaseifertia. Classification of 20 other species and varieties not recognised in the genus is discussed. Based on new collections of Dematiosporium aquaticum, the type species of Dematiosporium, the genus is emended to accommodate monodictys-like freshwater lignicolous fungi of the Savoryellales characterised by effuse colonies, holoblastic conidiogenous cells and dictyosporous, pigmented conidia with a pore in each cell. Study of additional new collections, cultures and DNA sequence data revealed several unknown species, which are proposed as taxonomic novelties in the Savoryellales and closely related Pleurotheciales. Ascotaiwania latericolla, Helicoascotaiwania lacustris and Pleurotheciella erumpens are described from terrestrial, lentic and lotic habitats from New Zealand and France, respectively. New combinations are proposed for Helicoascotaiwania farinosa and Neoascotaiwania fusiformis. Relationships and systematics of the Savoryellales are discussed in the light of recent phylogenies and morphological patterns newly linked with the order through cultural studies.
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27
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Tanney J, Seifert K. Mollisiaceae: An overlooked lineage of diverse endophytes. Stud Mycol 2020; 95:293-380. [PMID: 32855742 PMCID: PMC7426276 DOI: 10.1016/j.simyco.2020.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/15/2020] [Accepted: 02/15/2020] [Indexed: 01/04/2023] Open
Abstract
Mollisia is a taxonomically neglected discomycete genus (Helotiales, Leotiomycetes) of commonly encountered saprotrophs on decaying plant tissues throughout temperate regions. The combination of indistinct morphological characters, more than 700 names in the literature, and lack of reference DNA sequences presents a major challenge when working with Mollisia. Unidentified endophytes, including strains that produced antifungal or antiinsectan secondary metabolites, were isolated from conifer needles in New Brunswick and placed with uncertainty in Phialocephala and Mollisia, necessitating a more comprehensive treatment of these genera. In this study, morphology and multigene phylogenetic analyses were used to explore the taxonomy of Mollisiaceae, including Mollisia, Phialocephala, and related genera, using new field collections, herbarium specimens, and accessioned cultures and sequences. The phylogeny of Mollisiaceae was reconstructed and compared using the nuc internal transcribed spacer rDNA (ITS) barcode and partial sequences of the 28S nuc rDNA (LSU) gene, largest subunit of RNA polymerase II (RPB1), DNA topoisomerase I (TOP1), and the hypothetical protein Lipin/Ned1/Smp2 (LNS2). The results show that endophytism is common throughout the Mollisiaceae lineage in a diverse range of hosts but is infrequently attributed to Mollisia because of a paucity of reference sequences. Generic boundaries within Mollisiaceae are poorly resolved and based on phylogenetic evidence the family included species placed in Acephala, Acidomelania, Barrenia, Bispora, Cheirospora, Cystodendron, Fuscosclera, Hysteronaevia, Loramyces, Mollisia, Neopyrenopeziza, Obtectodiscus, Ombrophila, Patellariopsis, Phialocephala, Pulvinata, Tapesia (=Mollisia), and Trimmatostroma. Taxonomic novelties included the description of five novel Mollisia species and five novel Phialocephala species and the synonymy of Fuscosclera with Phialocephala, Acidomelania with Mollisia, and Loramycetaceae with Mollisiaceae.
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Affiliation(s)
- J.B. Tanney
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 Burnside Road, Victoria, British Columbia, V8Z 1M5, Canada
| | - K.A. Seifert
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
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Stadler M, Lambert C, Wibberg D, Kalinowski J, Cox RJ, Kolařík M, Kuhnert E. Intragenomic polymorphisms in the ITS region of high-quality genomes of the Hypoxylaceae (Xylariales, Ascomycota). Mycol Prog 2020. [DOI: 10.1007/s11557-019-01552-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
AbstractThe internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA) has been established (and is generally accepted) as a primary “universal” genetic barcode for fungi for many years, but the actual value for taxonomy has been heavily disputed among mycologists. Recently, twelve draft genome sequences, mainly derived from type species of the family Hypoxylaceae (Xylariales, Ascomycota) and the ex-epitype strain of Xylaria hypoxylon have become available during the course of a large phylogenomic study that was primarily aimed at establishing a correlation between the existing multi-gene-based genealogy with a genome-based phylogeny and the discovery of novel biosynthetic gene clusters encoding for secondary metabolites. The genome sequences were obtained using combinations of Illumina and Oxford nanopore technologies or PacBio sequencing, respectively, and resulted in high-quality sequences with an average N50 of 3.2 Mbp. While the main results will be published concurrently in a separate paper, the current case study was dedicated to the detection of ITS nrDNA copies in the genomes, in an attempt to explain certain incongruities and apparent mismatches between phenotypes and genotypes that had been observed during previous polyphasic studies. The results revealed that all of the studied strains had at least three copies of rDNA in their genomes, with Hypoxylon fragiforme having at least 19 copies of the ITS region, followed by Xylaria hypoxylon with at least 13 copies. Several of the genomes contained 2–3 copies that were nearly identical, but in some cases drastic differences, below 97% identity were observed. In one case, ascribable to the presence of a pseudogene, the deviations of the ITS sequences from the same genome resulted in only ca. 90% of overall homology. These results are discussed in the scope of the current trends to use ITS data for species recognition and segregation of fungi. We propose that additional genomes should be checked for such ITS polymorphisms to reassess the validity of this non-coding part of the fungal DNA for molecular identification.
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Basidioradulum mayi and B. tasmanicum spp. nov. (Hymenochaetales, Basidiomycota) from both sides of Bass Strait, Australia. Sci Rep 2020; 10:102. [PMID: 31919462 PMCID: PMC6952435 DOI: 10.1038/s41598-019-57061-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/21/2019] [Indexed: 11/08/2022] Open
Abstract
Basidioradulum was morphologically considered to be a synonym of Xylodon. Here, its independence within Hymenochaetales is confirmed from a phylogenetic perspective. Basidioradulum radula, the generic type, is widely distributed in Northern Hemisphere. Two Southern Hemisphere species close to B. radula are newly described as B. mayi and B. tasmanicum, respectively, from Victoria and Tasmania, Australia. Basidioradulum mayi differs from B. radula by lack of cystidia. Moreover, the hymenial surface of B. radula is normally much more strongly hydnoid than that of B. mayi. Basidioradulum tasmanicum is distinct from B. radula and B. mayi by having capitate cystidia, ellipsoid to subglobose basidiospores, and crystal-covered hyphae. Although morphologically distinct, the two new species isolated by Bass Strait have an almost identical ITS region, and could not be differentiated by nLSU- and ITS-based phylogenetic analyses. This case reminds us that basing phylogeny simply on the ITS as a barcode region may underestimate fungal species diversity.
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Haelewaters D, De Kesel A, Gorczak M, Bao K, Gort G, Zhao SY, Pfister DH. Laboulbeniales (Ascomycota) of the Boston Harbor Islands II (and Other Localities): Species Parasitizing Carabidae, and the Laboulbenia flagellata Species Complex. Northeast Nat (Steuben) 2019. [DOI: 10.1656/045.025.s906] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Skaltsas DN, Badotti F, Vaz ABM, Silva FFD, Gazis R, Wurdack K, Castlebury L, Góes-Neto A, Chaverri P. Exploration of stem endophytic communities revealed developmental stage as one of the drivers of fungal endophytic community assemblages in two Amazonian hardwood genera. Sci Rep 2019; 9:12685. [PMID: 31481728 PMCID: PMC6722055 DOI: 10.1038/s41598-019-48943-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Many aspects of the dynamics of tropical fungal endophyte communities are poorly known, including the influence of host taxonomy, host life stage, host defence, and host geographical distance on community assembly and composition. Recent fungal endophyte research has focused on Hevea brasiliensis due to its global importance as the main source of natural rubber. However, almost no data exist on the fungal community harboured within other Hevea species or its sister genus Micrandra. In this study, we expanded sampling to include four additional Hevea spp. and two Micrandra spp., as well as two host developmental stages. Through culture-dependent and -independent (metagenomic) approaches, a total of 381 seedlings and 144 adults distributed across three remote areas within the Peruvian Amazon were sampled. Results from both sampling methodologies indicate that host developmental stage had a greater influence in community assemblage than host taxonomy or locality. Based on FunGuild ecological guild assignments, saprotrophic and mycotrophic endophytes were more frequent in adults, while plant pathogens were dominant in seedlings. Trichoderma was the most abundant genus recovered from adult trees while Diaporthe prevailed in seedlings. Potential explanations for that disparity of abundance are discussed in relation to plant physiological traits and community ecology hypotheses.
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Affiliation(s)
- Demetra N Skaltsas
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland, 20742, USA.
- U.S. Department of Agriculture, Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland, 20705, USA.
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, MC-100-44, Oak Ridge, TN, 37831, USA.
| | - Fernanda Badotti
- Centro Federal de Educação Tecnológica de Minas Gerais, Departamento de Química, 30421-169, Belo Horizonte, Minas Gerais, 30421-169, Brazil
| | - Aline Bruna Martins Vaz
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, 31270-901, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Felipe Ferreira da Silva
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, 31270-901, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Romina Gazis
- University of Florida, Department of Plant Pathology, Tropical Research & Education Center, 18905 SW 280 Street, Homestead, Florida, 33031, USA
| | - Kenneth Wurdack
- Smithsonian Institution, Department of Botany, National Museum of Natural History, P.O. Box 37012, Washington, District of Columbia, 20013, USA
| | - Lisa Castlebury
- U.S. Department of Agriculture, Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland, 20705, USA
| | - Aristóteles Góes-Neto
- Centro Federal de Educação Tecnológica de Minas Gerais, Departamento de Química, 30421-169, Belo Horizonte, Minas Gerais, 30421-169, Brazil
| | - Priscila Chaverri
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland, 20742, USA
- Escuela de Biología, Centro de Investigaciones en Productos Naturales, Universidad de Costa Rica, San Pedro, San José, 11501, Costa Rica, USA
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Marin-Felix Y, Hernández-Restrepo M, Iturrieta-González I, García D, Gené J, Groenewald J, Cai L, Chen Q, Quaedvlieg W, Schumacher R, Taylor P, Ambers C, Bonthond G, Edwards J, Krueger-Hadfield S, Luangsa-ard J, Morton L, Moslemi A, Sandoval-Denis M, Tan Y, Thangavel R, Vaghefi N, Cheewangkoon R, Crous P. Genera of phytopathogenic fungi: GOPHY 3. Stud Mycol 2019; 94:1-124. [PMID: 31636728 PMCID: PMC6797016 DOI: 10.1016/j.simyco.2019.05.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.
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Key Words
- Allophoma pterospermicola Q. Chen & L. Cai
- Alternaria aconidiophora Iturrieta-González, Dania García & Gené
- Alternaria altcampina Iturrieta-González, Dania García & Gené
- Alternaria chlamydosporifera Iturrieta-González, Dania García & Gené
- Alternaria curvata Iturrieta-González, Dania García & Gené
- Alternaria fimeti Iturrieta-González, Dania García & Gené
- Alternaria inflata Iturrieta-González, Dania García & Gené
- Alternaria lawrencei Iturrieta-González, Dania García & Gené
- Alternaria montsantina Iturrieta-González, Dania García & Gené
- Alternaria pobletensis Iturrieta-González, Dania García & Gené
- Alternaria pseudoventricosa Iturrieta-González, Dania García & Gené
- Arezzomyces Y. Marín & Crous
- Arezzomyces cytisi (Wanas. et al.) Y. Marín & Crous
- Ascochyta chrysanthemi F. Stevens
- Brunneosphaerella roupeliae Crous
- DNA barcodes
- Elsinoe picconiae Crous
- Elsinoe veronicae Crous, Thangavel & Y. Marín
- Fungal systematics
- Globoramichloridium Y. Marín & Crous
- Globoramichloridium indicum (Subram.) Y. Marín & Crous
- Neosetophoma aseptata Crous, R.K. Schumach. & Y. Marín
- Neosetophoma phragmitis Crous, R.K. Schumach. & Y. Marín
- Neosetophoma sambuci Crous, R.K. Schumach. & Y. Marín
- Neostagonospora sorghi Crous & Y. Marín
- New taxa
- Parastagonospora novozelandica Crous, Thangavel & Y. Marín
- Parastagonospora phragmitis Crous & Y. Marín
- Pestalotia unicornis Cooke & Ellis
- Phaeosphaeria phoenicicola (Crous & Thangavel) Y. Marín & Crous
- Phaeosphaeriopsis aloes Crous & Y. Marín
- Phaeosphaeriopsis aloicola Crous & Y. Marín
- Phaeosphaeriopsis grevilleae Crous & Y. Marín
- Phaeosphaeriopsis pseudoagavacearum Crous & Y. Marín
- Pleiocarpon livistonae Crous & Quaedvl.
- Pyrenophora avenicola Y. Marín & Crous
- Pyrenophora cynosuri Y. Marín & Crous
- Pyrenophora nisikadoi Y. Marín & Crous
- Pyrenophora novozelandica Y. Marín & Crous
- Pyrenophora poae (Baudyš) Y. Marín & Crous
- Pyrenophora pseudoerythrospila Y. Marín & Crous
- Pyrenophora sieglingiae Y. Marín & Crous
- Pyrenophora variabilis Hern.-Restr. & Y. Marín
- Pyrenophora wirreganensis (Wallwork et al.) Y. Marín & Crous
- Rhynchosphaeria cupressi Nattrass et al
- Seiridium cupressi (Nattrass et al.) Bonthond, Sandoval-Denis & Crous
- Seiridium pezizoides (de Not.) Crous
- Septoriella agrostina (Mapook et al.) Y. Marín & Crous
- Septoriella artemisiae (Wanas. et al.) Y. Marín & Crous
- Septoriella arundinicola (Wanas. et al.) Y. Marín & Crous
- Septoriella arundinis (W.J. Li et al.) Y. Marín & Crous
- Septoriella bromi (Wijayaw. et al.) Y. Marín & Crous
- Septoriella dactylidicola Y. Marín & Crous
- Septoriella dactylidis (Wanas. et al.) Y. Marín & Crous
- Septoriella elongata (Wehm.) Y. Marín & Crous
- Septoriella forlicesenica (Thambug. et al.) Y. Marín & Crous
- Septoriella garethjonesii (Thambug. et al.) Y. Marín & Crous
- Septoriella germanica Crous, R.K. Schumach. & Y. Marín
- Septoriella hibernica Crous, Quaedvl. & Y. Marín
- Septoriella hollandica Crous, Quaedvl. & Y. Marín
- Septoriella italica (Thambug. et al.) Y. Marín & Crous
- Septoriella muriformis (Ariyaw. et al.) Y. Marín & Crous
- Septoriella neoarundinis Y. Marín & Crous
- Septoriella neodactylidis Y. Marín & Crous
- Septoriella pseudophragmitis Crous, Quaedvl. & Y. Marín
- Septoriella rosae (Mapook et al.) Y. Marín & Crous
- Septoriella subcylindrospora (W.J. Li et al.) Y. Marín & Crous
- Septoriella vagans (Niessl) Y. Marín & Crous
- Setophoma brachypodii Crous, R.K. Schumach. & Y. Marín
- Setophoma pseudosacchari Crous & Y. Marín
- Stemphylium rombundicum Moslemi, Y.P. Tan & P.W.J. Taylor
- Stemphylium truncatulae Moslemi, Y.P. Tan & P.W.J. Taylor
- Stemphylium waikerieanum Moslemi, Jacq. Edwards & P.W.J Taylor
- Vagicola arundinis Phukhams., Camporesi & K.D. Hyde
- Wingfieldomyces Y. Marín & Crous
- Wingfieldomyces cyperi (Crous & M.J. Wingf.) Y. Marín & Crous
- Zasmidium ducassei (R.G. Shivas et al.) Y. Marín & Crous
- Zasmidium thailandicum Crous
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Affiliation(s)
- Y. Marin-Felix
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201, Reus, Spain
| | - M. Hernández-Restrepo
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands
| | - I. Iturrieta-González
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201, Reus, Spain
| | - D. García
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201, Reus, Spain
| | - J. Gené
- Mycology Unit, Medical School and IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201, Reus, Spain
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - W. Quaedvlieg
- Royal Van Zanten, P.O. Box 265, 1430 AG, Aalsmeer, The Netherlands
| | | | - P.W.J. Taylor
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - C. Ambers
- P.O. Box 631, Middleburg, VA, 20118, USA
| | - G. Bonthond
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands
- Benthic Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Hohenbergstraße 2, 24105, Kiel, Germany
| | - J. Edwards
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio Centre, Bundoora, Victoria, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
| | - S.A. Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL, 35294, USA
| | - J.J. Luangsa-ard
- Plant Microbe Interaction Research Team, Integrative Crop Biotechnology and Management Research Group, Bioscience and Biotechnology for Agriculture, NSTDA 113, Thailand Science Park Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - L. Morton
- P.O. Box 5607, Charlottesville, VA, 22905, USA
| | - A. Moslemi
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Y.P. Tan
- Department of Agriculture and Fisheries, Biosecurity Queensland, Ecosciences Precinct, Dutton Park, 4012, QLD, Australia
- Microbiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - R. Thangavel
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland, 1140, New Zealand
| | - N. Vaghefi
- Centre for Crop Health, University of Southern Queensland, Queensland, 4350, Australia
| | - R. Cheewangkoon
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Tomé LMR, Badotti F, Assis GBN, Fonseca PLC, da Silva GA, da Silveira RMB, Costa-Rezende DH, Dos Santos ERD, de Carvalho Azevedo VA, Figueiredo HCP, Góes-Neto A. Proteomic fingerprinting for the fast and accurate identification of species in the Polyporoid and Hymenochaetoid fungi clades. J Proteomics 2019; 203:103390. [PMID: 31129267 DOI: 10.1016/j.jprot.2019.103390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 05/09/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022]
Abstract
Basidiomycotan fungi play significant roles in the biogeochemical cycle of carbon as wood decomposers and are used in the food industry for mushroom production and in biotechnology for the production of diverse bioactive compounds and bioremediation. The correct identification of basidiomycotan isolates is crucial for understanding their biology and being able to expand their applications. Currently, the identification of these organisms is performed by analyzing morphological and genomic characteristics, primarily those based on DNA biomarkers. Despite their efficiency, such methods require considerable expertise and are both time-consuming and error-prone (multistep workflow). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged in the last decade as an accurate, fast, and powerful alternative for the identification of microorganisms. MALDI-TOF MS has been widely applied for the identification and taxonomical characterization of both bacteria and ascomycotan fungi from clinical origins. However, species of Basidiomycota have been poorly evaluated using this method. In the present study, we assessed the performance of MALDI-TOF MS using basidiomycotan isolates of two distinct taxonomical families: Polyporaceae and Hymenochaetaceae. Using a simple protocol, which eliminates the protein extraction step, we obtained high-quality mass spectra data and demonstrated that this method is efficient for the discrimination of isolates at the species level. SIGNIFICANCE: In this study, the MALDI-TOF mass spectrometry was employed to test its accuracy on the recognition of fungal species with high biotechnological and environmental interest. Using a simple and fast protocol, we obtained high-quality mass-spectra (protein fingerprinting) and proved that MALDI-TOF MS is sufficiently robust to the identification at species level and to evaluate the relationships among the isolates of the polyporoid and hymenochaetoid clades (Basidiomycota).
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Affiliation(s)
- Luiz Marcelo Ribeiro Tomé
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Belo Horizonte, MG, Brazil
| | - Gabriella Borba Netto Assis
- AQUACEN - Laboratório Oficial de Diagnóstico de Doenças de Animais Aquáticos do Ministério da Agricultura, Pecuária e Abastecimento, Escola de Veterinária da Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Paula Luize Camargos Fonseca
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Genivaldo Alves da Silva
- Laboratory of Mycology, Botany Department, Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, RS, Brazil
| | - Rosa Mara Borges da Silveira
- Laboratory of Mycology, Botany Department, Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, RS, Brazil
| | | | | | - Vasco Ariston de Carvalho Azevedo
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Henrique Cesar Pereira Figueiredo
- AQUACEN - Laboratório Oficial de Diagnóstico de Doenças de Animais Aquáticos do Ministério da Agricultura, Pecuária e Abastecimento, Escola de Veterinária da Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
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Meiklejohn KA, Damaso N, Robertson JM. Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials. PLoS One 2019; 14:e0217084. [PMID: 31216285 PMCID: PMC6584008 DOI: 10.1371/journal.pone.0217084] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/04/2019] [Indexed: 11/19/2022] Open
Abstract
Taxonomic identification of biological materials can be achieved through DNA barcoding, where an unknown "barcode" sequence is compared to a reference database. In many disciplines, obtaining accurate taxonomic identifications can be imperative (e.g., evolutionary biology, food regulatory compliance, forensics). The Barcode of Life DataSystems (BOLD) and GenBank are the main public repositories of DNA barcode sequences. In this study, an assessment of the accuracy and reliability of sequences in these databases was performed. To achieve this, 1) curated reference materials for plants, macro-fungi and insects were obtained from national collections, 2) relevant barcode sequences (rbcL, matK, trnH-psbA, ITS and COI) from these reference samples were generated and used for searching against both databases, and 3) optimal search parameters were determined that ensure the best match to the known species in either database. While GenBank outperformed BOLD for species-level identification of insect taxa (53% and 35%, respectively), both databases performed comparably for plants and macro-fungi (~81% and ~57%, respectively). Results illustrated that using a multi-locus barcode approach increased identification success. This study outlines the utility of the BLAST search tool in GenBank and the BOLD identification engine for taxonomic identifications and identifies some precautions needed when using public sequence repositories in applied scientific disciplines.
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Affiliation(s)
- Kelly A. Meiklejohn
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, Virginia, United States of America
| | - Natalie Damaso
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, Virginia, United States of America
| | - James M. Robertson
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, Quantico, Virginia, United States of America
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Sochorová Z, Döbbeler P, Sochor M, van Rooy J. Octosporaconidiophora (Pyronemataceae) - a new species from South Africa and the first report of anamorph in bryophilous Pezizales. MycoKeys 2019; 54:49-76. [PMID: 31231165 PMCID: PMC6579791 DOI: 10.3897/mycokeys.54.34571] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/26/2019] [Indexed: 02/04/2023] Open
Abstract
Octosporaconidiophora is described as a new species, based on collections from South Africa. It is characterised by apothecia with a distinct margin, smooth or finely warted ellipsoid ascospores, stiff, thick-walled hyaline hairs, warted mycelial hyphae and growth on pleurocarpous mosses Trichosteleumperchlorosum and Sematophyllumbrachycarpum (Hypnales) on decaying wood in afromontane forests. It is the first species of bryophilous Pezizales in which an anamorph has been observed; it produces long, claviform, curved, hyaline and transversely septate conidia. Three other cryptic species of Octospora were detected using three molecular markers (LSU and SSU nrDNA and EF1α), but these could not be distinguished phenotypically. These are not described formally here and an informal species aggregate O.conidiophora agg. is established for them. The new species and finds of Lamprosporacampylopodis growing on Campylopuspyriformis and Neottiellaalbocincta on Atrichumandrogynum represent the first records of bryophilous Pezizales in South Africa.
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Affiliation(s)
- Zuzana Sochorová
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic Crop Research Institute, Centre of the Region Haná for Biotechnological and Agricultural Research Olomouc Czech Republic.,Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 29, Olomouc, CZ-78371, Czech Republic Universität München München Germany
| | - Peter Döbbeler
- Ludwig-Maximilians-Universität München, Systematische Botanik und Mykologie, Menzinger Straße 67, München, D-80638, Germany Palacký University Olomouc Olomouc Czech Republic
| | - Michal Sochor
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 29, Olomouc, CZ-78371, Czech Republic Universität München München Germany
| | - Jacques van Rooy
- National Herbarium, South African National Biodiversity Institute (SANBI), Private Bag X101, Pretoria 0001, South Africa National Herbarium, South African National Biodiversity Institute Pretoria South Africa.,School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, PO WITS 2050, South Africa University of the Witwa-tersrand Johannesburg South Africa
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Wu B, Hussain M, Zhang W, Stadler M, Liu X, Xiang M. Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi. Mycology 2019; 10:127-140. [PMID: 31448147 PMCID: PMC6691916 DOI: 10.1080/21501203.2019.1614106] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/22/2019] [Indexed: 01/09/2023] Open
Abstract
The global bio-diversity of fungi has been extensively investigated and their species number has been estimated. Notably, the development of molecular phylogeny has revealed an unexpected fungal diversity and utilisation of culture-independent approaches including high-throughput amplicon sequencing has dramatically increased number of fungal operational taxonomic units. A number of novel taxa including new divisions, classes, orders and new families have been established in last decade. Many cryptic species were identified by molecular phylogeny. Based on recently generated data from culture-dependent and -independent survey on same samples, the fungal species on the earth were estimated to be 12 (11.7-13.2) million compared to 2.2-3.8 million species recently estimated by a variety of the estimation techniques. Moreover, it has been speculated that the current use of high-throughput sequencing techniques would reveal an even higher diversity than our current estimation. Recently, the formal classification of environmental sequences and permission of DNA sequence data as fungal names' type were proposed but strongly objected by the mycologist community. Surveys on fungi in unusual niches have indicated that many previously regarded "unculturable fungi" could be cultured on certain substrates under specific conditions. Moreover, the high-throughput amplicon sequencing, shotgun metagenomics and a single-cell genomics could be a powerful means to detect novel taxa. Here, we propose to separate the fungal types into physical type based on specimen, genome DNA (gDNA) type based on complete genome sequence of culturable and uncluturable fungal specimen and digital type based on environmental DNA sequence data. The physical and gDNA type should have priority, while the digital type can be temporal supplementary before the physical type and gDNA type being available. The fungal name based on the "digital type" could be assigned as the "clade" name + species name. The "clade" name could be the name of genus, family or order, etc. which the sequence of digital type affiliates to. Facilitating future cultivation efforts should be encouraged. Also, with the advancement in knowledge of fungi inhabiting various environments mostly because of rapid development of new detection technologies, more information should be expected for fungal diversity on our planet.
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Affiliation(s)
- Bing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Muzammil Hussain
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Weiwei Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Marin-Felix Y, Hernández-Restrepo M, Wingfield M, Akulov A, Carnegie A, Cheewangkoon R, Gramaje D, Groenewald J, Guarnaccia V, Halleen F, Lombard L, Luangsa-ard J, Marincowitz S, Moslemi A, Mostert L, Quaedvlieg W, Schumacher R, Spies C, Thangavel R, Taylor P, Wilson A, Wingfield B, Wood A, Crous P. Genera of phytopathogenic fungi: GOPHY 2. Stud Mycol 2019; 92:47-133. [PMID: 29997401 PMCID: PMC6031069 DOI: 10.1016/j.simyco.2018.04.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
This paper represents the second contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information regarding the pathology, distribution, hosts and disease symptoms for the treated genera. In addition, primary and secondary DNA barcodes for the currently accepted species are included. This second paper in the GOPHY series treats 20 genera of phytopathogenic fungi and their relatives including: Allantophomopsiella, Apoharknessia, Cylindrocladiella, Diaporthe, Dichotomophthora, Gaeumannomyces, Harknessia, Huntiella, Macgarvieomyces, Metulocladosporiella, Microdochium, Oculimacula, Paraphoma, Phaeoacremonium, Phyllosticta, Proxypiricularia, Pyricularia, Stenocarpella, Utrechtiana and Wojnowiciella. This study includes the new genus Pyriculariomyces, 20 new species, five new combinations, and six typifications for older names.
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Key Words
- 26 new taxa
- Apoharknessia eucalypti Crous & M.J. Wingf.
- Cylindrocladiella addiensis L. Lombard & Crous
- Cylindrocladiella nauliensis L. Lombard & Crous
- DNA barcodes
- Diaporthe heterophyllae Guarnaccia & Crous
- Diaporthe racemosae A.R. Wood, Guarnaccia & Crous
- Dichotomophthora basellae Hern.-Restr., Cheew. & Crous
- Dichotomophthora brunnea Hern.-Restr. & Crous
- Fungal systematics
- Harknessia bourbonica Crous & M.J. Wingf.
- Harknessia corymbiae Crous & A.J. Carnegie
- Harknessia cupressi Crous & R.K. Schumach.
- Harknessia pilularis Crous & A.J. Carnegie
- Helminthosporium arundinaceum Corda
- Huntiella abstrusa A.M. Wilson, Marinc., M.J. Wingf.
- Macgarvieomyces luzulae (Ondřej) Y. Marín, Akulov & Crous
- Metulocladosporiella chiangmaiensis Y. Marín, Cheew. & Crous
- Metulocladosporiella malaysiana Y. Marín & Crous
- Metulocladosporiella musigena Y. Marín, Cheew. & Crous
- Metulocladosporiella samutensis Y. Marín, Luangsa-ard & Crous
- Microdochium novae-zelandiae Hern.-Restr., Thangavel & Crous
- Oculimacula acuformis (Nirenberg) Y. Marín & Crous
- Phaeoacremonium pravum C.F.J. Spies, L. Mostert & Halleen
- Phomopsis pseudotsugae M. Wilson
- Phyllosticta iridigena Y. Marín & Crous
- Phyllosticta persooniae Y. Marín & Crous
- Pyricularia luzulae Ondřej
- Pyricularia zingiberis Y. Nishik
- Pyriculariomyces Y. Marín, M.J. Wingf. & Crous
- Pyriculariomyces asari (Crous & M.J. Wingf.) Y. Marín, M.J. Wingf. & Crous
- Six new typifications
- Utrechtiana arundinacea (Corda) Crous, Quaedvl. & Y. Marín
- Utrechtiana constantinescui (Melnik & Shabunin) Crous & Y. Marín
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Affiliation(s)
- Y. Marin-Felix
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, Pretoria, 0002, South Africa
| | - M. Hernández-Restrepo
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - M.J. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, Pretoria, 0002, South Africa
| | - A. Akulov
- V.N. Karasin National University of Kharkiv, Svobody sq. 4, Kharkiv 61077, Ukraine
| | - A.J. Carnegie
- Forest Science, NSW Department of Primary Industries, Locked Bag 5123, Parramatta, New South Wales 2124, Australia
| | - R. Cheewangkoon
- Department of Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - D. Gramaje
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas, Universidad de la Rioja, Gobierno de La Rioja, 26071 Logroño, La Rioja, Spain
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - V. Guarnaccia
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - F. Halleen
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- Plant Protection Division, ARC Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch 7599, South Africa
| | - L. Lombard
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - J. Luangsa-ard
- Microbe Interaction and Ecology Laboratory, Biodiversity and Biotechnological Resource Research Unit (BBR), BIOTEC, NSTDA 113, Thailand Science Park Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - S. Marincowitz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, Pretoria, 0002, South Africa
| | - A. Moslemi
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne 3010, Melbourne, Victoria, Australia
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - W. Quaedvlieg
- Naktuinbouw, Sotaweg 22, 2371 GD Roelofarendsveen, the Netherlands
| | | | - C.F.J. Spies
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- Plant Protection Division, ARC Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch 7599, South Africa
| | - R. Thangavel
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - P.W.J. Taylor
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne 3010, Melbourne, Victoria, Australia
| | - A.M. Wilson
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, Pretoria, 0002, South Africa
| | - B.D. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, Pretoria, 0002, South Africa
| | - A.R. Wood
- ARC – Plant Protection Research Institute, Private Bag X5017, Stellenbosch 7599, South Africa
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, Pretoria, 0002, South Africa
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Meher PK, Sahu TK, Gahoi S, Tomar R, Rao AR. funbarRF: DNA barcode-based fungal species prediction using multiclass Random Forest supervised learning model. BMC Genet 2019; 20:2. [PMID: 30616524 PMCID: PMC6323839 DOI: 10.1186/s12863-018-0710-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 12/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identification of unknown fungal species aids to the conservation of fungal diversity. As many fungal species cannot be cultured, morphological identification of those species is almost impossible. But, DNA barcoding technique can be employed for identification of such species. For fungal taxonomy prediction, the ITS (internal transcribed spacer) region of rDNA (ribosomal DNA) is used as barcode. Though the computational prediction of fungal species has become feasible with the availability of huge volume of barcode sequences in public domain, prediction of fungal species is challenging due to high degree of variability among ITS regions within species. RESULTS A Random Forest (RF)-based predictor was built for identification of unknown fungal species. The reference and query sequences were mapped onto numeric features based on gapped base pair compositions, and then used as training and test sets respectively for prediction of fungal species using RF. More than 85% accuracy was found when 4 sequences per species in the reference set were utilized; whereas it was seen to be stabilized at ~88% if ≥7 sequence per species in the reference set were used for training of the model. The proposed model achieved comparable accuracy, while evaluated against existing methods through cross-validation procedure. The proposed model also outperformed several existing models used for identification of different species other than fungi. CONCLUSIONS An online prediction server "funbarRF" is established at http://cabgrid.res.in:8080/funbarrf/ for fungal species identification. Besides, an R-package funbarRF ( https://cran.r-project.org/web/packages/funbarRF/ ) is also available for prediction using high throughput sequence data. The effort put in this work will certainly supplement the future endeavors in the direction of fungal taxonomy assignments based on DNA barcode.
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Affiliation(s)
- Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Tanmaya Kumar Sahu
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Shachi Gahoi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Ruchi Tomar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
- Department of Bioinformatics, Janta Vedic College, Baraut, Baghpat, Uttar Pradesh 250611 India
| | - Atmakuri Ramakrishna Rao
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
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Li Z, Fu J, Zhou R, Wang D. Effects of phenolic acids from ginseng rhizosphere on soil fungi structure, richness and diversity in consecutive monoculturing of ginseng. Saudi J Biol Sci 2018; 25:1788-1794. [PMID: 30591801 PMCID: PMC6303186 DOI: 10.1016/j.sjbs.2018.07.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 12/05/2022] Open
Abstract
Ginseng yield and quality are seriously compromised by consecutive monoculturing in northeastern China. The imbalance of soil fungi communities and autotoxicity of ginseng are the major factors in consecutive monoculturing ginseng crops. Soil fungal communities were identified using Illumina MiSeq sequencing, applied to soils that consecutively cultured ginseng (CCG) for six years and new forest soil (NFS), or receiving application of phenolic acids (PAs). The CCG field received five treatments with five different phenolic acids, including gallic acid (GA), salicylic acid (SA), 3-phenylpropionic acid (3-PA), benzoic acid (BA) and cinnamic acid (CA), which were detected from ginseng rhizosphere in consecutive cropping soil. Fungal richness, fungi diversity, community composition, relative taxon abundances, root rot disease, and growth rate were compared among the different treatments. 579 fungal operational taxonomic units at 97% ITS sequence identity were found among 201,617 sequence reads derived from 18 separate soil samples. Members of the phylum Ascomycota dominated the soil fungal communities, and putative pathogens, such as Fusarium, Gibberella and Nectriaceae_unclassified which may include the abundant sexual morph of Cylindrocarpon destructans, showed higher relative abundances in the CCG fields. Compared to the CCG and NFS fields, PAs (except CA) enhanced the fungi richness and decreased fungi diversity. Cluster analysis indicated that the PAs (except CA) changed the fungi structure in a uniform way. PAs stimulate root rot disease and enhance disease severity, restricting plant growth. The results suggest that the PAs (except CA) may enhance the fungi richness, decrease the fungi diversity and changed the fungi structure to increase fungal pathogen loads, which could explain the declined yield and quality of ginseng in consecutively monocultured ginseng crops.
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Affiliation(s)
| | - Junfan Fu
- Department of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
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Idondo LF, Colombo RP, Recchi M, Silvani VA, Pérgola M, Martínez A, Godeas AM. Detection of arbuscular mycorrhizal fungi associated with pecan ( Caryaillinoinensis) trees by molecular and morphological approaches. MycoKeys 2018:73-88. [PMID: 30564053 PMCID: PMC6286380 DOI: 10.3897/mycokeys.42.26118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/11/2018] [Indexed: 01/17/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungal community associated with pecan (Caryaillinoinensis) roots and rhizospheric soils was assessed by spore isolation and morphological characterisation and by pyrosequencing of AM molecular markers. The AM fungal community associated with pecan growing in the field, was always more diverse than that associated with pecan growing in containers. This was not observed when AM richness was studied, suggesting that soil disturbance by a reduction in host plant richness leads to a less equitable distribution of AM fungal species, in contrast to natural soils. The chosen primers (AMV4.5F/AMDGR) for pyrosequencing showed high AM fungal specificity. Based on 97% sequence similarity, 49 operational taxonomic units (MOTUs) were obtained and, amongst these, 41 MOTUs corresponded to the Glomeromycotaphylum. The number of obtained AM sequences ranged from 2164, associated with field samples, to 5572 obtained from pecan trap pot culture samples, defining 30 and 29 MOTUs, respectively. Richness estimated by conventional species identification was 6 and 9 AM fungal species in soil and pot samples, respectively. Claroideoglomuslamellosum, Funneliformismosseae and Entrophosporainfrequens were the only taxa detected using both techniques. Predominant sequences in the pecan rhizosphere samples, such as Rhizoglomusirregulare and other less abundant (Dominikiairanica, Dominikiaindica, Sclerocystissinuosa, Paraglomuslaccatum), were detected only by pyrosequencing. Detection of AM fungal species based on spore morphology, in combination with molecular approaches, provides a more comprehensive estimate of fungal community composition.
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Affiliation(s)
- L Fernández Idondo
- Laboratorio de Microbiología del Suelo. Instituto de Biodiversidad y Biología Experimental Aplicada. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, 4to piso, Pabellón 2. 1428. Buenos Aires. Argentina Universidad de Buenos Aires Buenos Aires Argentina
| | - R P Colombo
- Laboratorio de Microbiología del Suelo. Instituto de Biodiversidad y Biología Experimental Aplicada. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, 4to piso, Pabellón 2. 1428. Buenos Aires. Argentina Universidad de Buenos Aires Buenos Aires Argentina
| | - M Recchi
- Laboratorio de Microbiología del Suelo. Instituto de Biodiversidad y Biología Experimental Aplicada. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, 4to piso, Pabellón 2. 1428. Buenos Aires. Argentina Universidad de Buenos Aires Buenos Aires Argentina
| | - V A Silvani
- Laboratorio de Microbiología del Suelo. Instituto de Biodiversidad y Biología Experimental Aplicada. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, 4to piso, Pabellón 2. 1428. Buenos Aires. Argentina Universidad de Buenos Aires Buenos Aires Argentina
| | - M Pérgola
- Laboratorio de Microbiología del Suelo. Instituto de Biodiversidad y Biología Experimental Aplicada. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, 4to piso, Pabellón 2. 1428. Buenos Aires. Argentina Universidad de Buenos Aires Buenos Aires Argentina
| | - A Martínez
- Laboratorio de Microbiología del Suelo. Instituto de Biodiversidad y Biología Experimental Aplicada. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, 4to piso, Pabellón 2. 1428. Buenos Aires. Argentina Universidad de Buenos Aires Buenos Aires Argentina
| | - A M Godeas
- Laboratorio de Microbiología del Suelo. Instituto de Biodiversidad y Biología Experimental Aplicada. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, 4to piso, Pabellón 2. 1428. Buenos Aires. Argentina Universidad de Buenos Aires Buenos Aires Argentina
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Bates ST, Miller AN, the Macrofungi Collections and Microfungi Collections Consor . The protochecklist of North American nonlichenized Fungi. Mycologia 2018. [DOI: 10.1080/00275514.2018.1515410] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Scott T. Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, Indiana 46391
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, Illinois 61820
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Cuscó A, Catozzi C, Viñes J, Sanchez A, Francino O. Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon. F1000Res 2018; 7:1755. [PMID: 30815250 PMCID: PMC6372929 DOI: 10.12688/f1000research.16817.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/30/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples often contain DNA from other sources, such as the host or the environment. The usual approach is sequencing specific hypervariable regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. Here, we aim to assess long-amplicon PCR-based approaches for assigning taxonomy at the genus and species level. We use Nanopore sequencing with two different markers: full-length 16S rRNA (~1,500 bp) and the whole rrn operon (16S rRNA-ITS-23S rRNA; 4,500 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities (HM-783D, Bei Resources; D6306, ZymoBIOMICS™) and two pools of low-biomass samples (dog skin from either the chin or dorsal back), using the MinION™ sequencer 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using the WIMP workflow on EPI2ME or Minimap2 software with rrn database. Results: The full-length 16S rRNA and the rrn operon were used to retrieve the microbiota composition at the genus and species level from the bacterial isolate, mock communities and complex skin samples. For the Staphylococcus pseudintermedius isolate, when using EPI2ME, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the rrn operon marker, and in ~68% of the cases with the 16S rRNA gene. In both skin microbiota samples, we detected many species with an environmental origin. In chin, we found different Pseudomonas species in high abundance, whereas in dorsal skin there were more taxa with lower abundances. Conclusions: Both full-length 16S rRNA and the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, using the rrn operon would be the best choice.
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Affiliation(s)
- Anna Cuscó
- Vetgenomics, SL, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Carlotta Catozzi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milano, Italy
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Joaquim Viñes
- Vetgenomics, SL, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Armand Sanchez
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
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Cuscó A, Catozzi C, Viñes J, Sanchez A, Francino O. Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon. F1000Res 2018; 7:1755. [PMID: 30815250 PMCID: PMC6372929 DOI: 10.12688/f1000research.16817.2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples are prone to contain DNA from other sources (e.g. host or environment). The usual approach is sequencing short regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. To achieve an increased taxonomic resolution, we aim to develop long-amplicon PCR-based approaches using Nanopore sequencing. We assessed two different genetic markers: the full-length 16S rRNA (~1,500 bp) and the 16S-ITS-23S region from the rrn operon (4,300 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities and two pools of low-biomass samples (dog skin). Nanopore sequencing was performed on MinION™ using the 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using EPI2ME or Minimap2 with rrn database. Consensus sequences of the 16S-ITS-23S genetic marker were obtained using canu. Results: The full-length 16S rRNA and the 16S-ITS-23S region of the rrn operon were used to retrieve the microbiota composition of the samples at the genus and species level. For the Staphylococcus pseudintermedius isolate, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the16S-ITS-23S genetic marker, and in ~68%, with the 16S rRNA gene when using EPI2ME. Using mock communities, we found that the full-length 16S rRNA gene represented better the abundances of a microbial community; whereas, 16S-ITS-23S obtained better resolution at the species level. Finally, we characterized low-biomass skin microbiota samples and detected species with an environmental origin. Conclusions: Both full-length 16S rRNA and the 16S-ITS-23S of the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, targeting the 16S-ITS-23S of the rrn operon would be the best choice.
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Affiliation(s)
- Anna Cuscó
- Vetgenomics, SL, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Carlotta Catozzi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milano, Italy
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Joaquim Viñes
- Vetgenomics, SL, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Armand Sanchez
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain
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Ahrendt SR, Quandt CA, Ciobanu D, Clum A, Salamov A, Andreopoulos B, Cheng JF, Woyke T, Pelin A, Henrissat B, Reynolds NK, Benny GL, Smith ME, James TY, Grigoriev IV. Leveraging single-cell genomics to expand the fungal tree of life. Nat Microbiol 2018; 3:1417-1428. [PMID: 30297742 PMCID: PMC6784888 DOI: 10.1038/s41564-018-0261-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 09/03/2018] [Indexed: 11/09/2022]
Abstract
Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across the fungal tree of life using a new single-cell genomics pipeline. We show that, despite a large variation in genome and gene space recovery from each single amplified genome (SAG), ≥90% can be recovered by combining multiple SAGs. SAGs provide robust placement for early-diverging lineages and infer a diploid ancestor of fungi. Early-diverging fungi share metabolic deficiencies and show unique gene expansions correlated with parasitism and unculturability. Single-cell genomics holds great promise in exploring fungal diversity, life cycles and metabolic potential.
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Affiliation(s)
- Steven R Ahrendt
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Doina Ciobanu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Bill Andreopoulos
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Adrian Pelin
- Ottawa Hospital Research Institute, Centre for Innovative Cancer Research, Ottawa, Ontario, Canada
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR 7857 CNRS, Aix-Marseille University, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nicole K Reynolds
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Gerald L Benny
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA. .,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
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Irga PJ, Barker K, Torpy FR. Conservation mycology in Australia and the potential role of citizen science. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2018; 32:1031-1037. [PMID: 29687520 DOI: 10.1111/cobi.13121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 04/10/2018] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
Fungi are undoubtedly important for ecosystem functioning; however, they have been omitted or given scant attention in most biodiversity policy documents, management plans, and formal conservation schedules throughout the world. This oversight may be due to a general lack of awareness in the scientific community and compounded by a scarcity of mycology-associated curricula at the tertiary level and a lack of mycologists in research institutions. Although molecular techniques advance the systematic cataloging of fungi and facilitate insights into fungal communities, the scarcity of professional mycologists in the environmental sciences hampers conservation efforts. Conversely, citizen science initiatives are making significant contributions to the mycology discipline by increasing awareness and extending the scope of fungal surveys. Future research by professional and amateur mycologists into the distribution of fungi and their function in ecosystems will help identify wider and more effective conservation goals.
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Affiliation(s)
- Peter J Irga
- School of Civil and Environmental Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, P.O. Box 123, 81 Broadway, Sydney, NSW 2007, Australia
| | - Katherine Barker
- School of Life Sciences, Faculty of Science, University of Technology Sydney, P.O. Box 123, 15 Broadway, Sydney, NSW 2007, Australia
| | - Fraser R Torpy
- School of Life Sciences, Faculty of Science, University of Technology Sydney, P.O. Box 123, 15 Broadway, Sydney, NSW 2007, Australia
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Niskanen T, Liimatainen K, Nuytinck J, Kirk P, Ibarguren IO, Garibay-Orijel R, Norvell L, Huhtinen S, Kytövuori I, Ruotsalainen J, Niemelä T, Ammirati JF, Tedersoo L. Identifying and naming the currently known diversity of the genus Hydnum, with an emphasis on European and North American taxa. Mycologia 2018; 110:890-918. [DOI: 10.1080/00275514.2018.1477004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Tuula Niskanen
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey TW9 3AB, United Kingdom
| | - Kare Liimatainen
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey TW9 3AB, United Kingdom
- Department of Biosciences, Plant Biology, P.O. Box 65, FI-00014 University of Helsinki, Helsinki, Finland
| | - Jorinde Nuytinck
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Paul Kirk
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey TW9 3AB, United Kingdom
| | - Ibai Olariaga Ibarguren
- Department of Biology and Geology, Physics and Inorganic Chemistry, King Juan Carlos University, c/Tulipan 28933, Móstoles, Spain
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, A.P. 70-233, C.P. 04510 México, D.F., México
| | - Lorelei Norvell
- Pacific Northwest Mycology Service, 6720 NW Skylne Boulevard, Portland, Oregon 97229
| | - Seppo Huhtinen
- Biodiversity Unit, Herbarium, University of Turku, FI-20014 Turku, Finland
| | - Ilkka Kytövuori
- Botanical Museum, P.O. Box 7, FI-00014 University of Helsinki, Helsinki, Finland
| | | | - Tuomo Niemelä
- Botanical Museum, P.O. Box 7, FI-00014 University of Helsinki, Helsinki, Finland
| | - Joseph F. Ammirati
- Department of Biology, Box 351800, University of Washington, Seattle, Washington 98195-1800
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, 14A Ravila, 50411 Tartu, Estonia
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Arroyo AS, López-Escardó D, Kim E, Ruiz-Trillo I, Najle SR. Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00099] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Hongsanan S, Jeewon R, Purahong W, Xie N, Liu JK, Jayawardena RS, Ekanayaka AH, Dissanayake A, Raspé O, Hyde KD, Stadler M, Peršoh D. Can we use environmental DNA as holotypes? FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0404-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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