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Leiva AM, Pardo JM, Arinaitwe W, Newby J, Vongphachanh P, Chittarath K, Oeurn S, Thi Hang L, Gil-Ordóñez A, Rodriguez R, Cuellar WJ. Ceratobasidium sp. is associated with cassava witches' broom disease, a re-emerging threat to cassava cultivation in Southeast Asia. Sci Rep 2023; 13:22500. [PMID: 38110543 PMCID: PMC10728180 DOI: 10.1038/s41598-023-49735-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
Cassava witches' broom disease (CWBD) is a devastating disease of cassava in Southeast Asia (SEA), of unknown etiology. Affected plants show reduced internodal length, proliferation of leaves and weakening of stems. This results in poor germination of infected stem cuttings (i.e., planting material) and significant reductions in fresh root yields and starch content, causing economic losses for farmers and processors. Using a metagenomic approach, we identified a fungus belonging to the Ceratobasidium genus, sharing more than 98.3-99.7% nucleotide identity at the Internal Transcribed Spacer (ITS), with Ceratobasidium theobromae a pathogen causing similar symptoms in cacao. Microscopy analysis confirmed the identity of the fungus and specific designed PCR tests readily showed (1) Ceratobasidium sp. of cassava is strongly associated with CWBD symptoms, (2) the fungus is present in diseased samples collected since the first recorded CWBD outbreaks in SEA and (3) the fungus is transmissible by grafting. No phytoplasma sequences were detected in diseased plants. Current disease management efforts include adjustment of quarantine protocols and guarantee the production and distribution of Ceratobasidium-free planting material. Implications of related Ceratobasidium fungi, infecting cassava, and cacao in SEA and in other potential risk areas are discussed.
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Affiliation(s)
- Ana M Leiva
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Juan M Pardo
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Warren Arinaitwe
- Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cassava Program Asia Office, P.O. Box 783, Vientiane, Lao PDR
| | - Jonathan Newby
- Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cassava Program Asia Office, P.O. Box 783, Vientiane, Lao PDR
| | - Pinkham Vongphachanh
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, P.O. Box 811, Vientiane, Lao PDR
| | - Khonesavanh Chittarath
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, P.O. Box 811, Vientiane, Lao PDR
| | - Samoul Oeurn
- Plant Protection Sanitary and Phytosanitary Department, General Directorate of Agriculture (GDA), Phnom Penh, 120406, Cambodia
| | - Le Thi Hang
- Plant Protection Research Institute (PPRI), Duc Thang Bac Tu Liem, Hanoi, 100000, Vietnam
| | - Alejandra Gil-Ordóñez
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Rafael Rodriguez
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Wilmer J Cuellar
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Palacıoğlu G, Alkan M, Derviş S, Bayraktar H, Özer G. Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism. Mol Biol Rep 2023; 50:8271-8279. [PMID: 37578578 DOI: 10.1007/s11033-023-08735-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi. MATERIALS AND METHODS This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers. RESULTS The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei's diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers. CONCLUSIONS SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.
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Affiliation(s)
- Gülsüm Palacıoğlu
- Department of Plant Protection, Faculty of Agriculture, Şırnak University, Şırnak, Turkey
| | - Mehtap Alkan
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Sibel Derviş
- Department of Plant and Animal Production, Vocational School of Kızıltepe, Mardin Artuklu University, Mardin, Turkey
| | - Harun Bayraktar
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey.
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
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Al Harethi AA, Abdullah QYM, Al Jobory HJ, Al Aquil SA, Arafa RA. First report of molecular identification of Phytophthora infestans causing potato late blight in Yemen. Sci Rep 2023; 13:16365. [PMID: 37773211 PMCID: PMC10541906 DOI: 10.1038/s41598-023-43510-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023] Open
Abstract
Late blight, caused by Phytophthora infestans, is one of the most destructive potato diseases in the world. In Yemen, identification of P. infestans still depends on a visual survey and external examination of late blight symptoms. The objective of this study was to isolate and identify P. infestans by using advanced methods. We collected 71 disease samples and isolated the pathogen using the tuber slice method. To identify an isolated pathogen, we performed morphological characterization and gene sequence analysis of the coding genes for internal transcribed spacers. We used Koch's hypotheses to confirm the previous results. In our study. The morphological characters of the mycelium pattern of P. infestans isolates in Yemen were profusely branching, fluffy, and white. The sporangia showed remarkable limoniform papillate sporangial shape. with average length and width of 30.6 and 28.6 µm, respectively. The sequences analysis showed high homology with a degree of identity ranging from 98 to 100% to the database sequences on GenBank. Pathogenicity tests showed that the P. infestans was the causal agent. To our knowledge, this is the first study of the isolation and characterization of P. infestans in Yemen.
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Affiliation(s)
- Amira A Al Harethi
- Department of Biological Science, Faculty of Science, Sana'a University, Sana'a, Yemen.
| | - Qais Y M Abdullah
- Department of Biological Science, Faculty of Science, Sana'a University, Sana'a, Yemen
| | - Hala J Al Jobory
- Department of Biological Science, Faculty of Science, Sana'a University, Sana'a, Yemen
| | - Samar A Al Aquil
- Department of Physics, Faculty of Science, Sana'a University, Sana'a, Yemen
| | - Ramadan A Arafa
- Plant Pathology Research Institute, Agricultural Research Center, Giza, 12619, Egypt
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Rúa-Giraldo ÁL. Fungal taxonomy: A puzzle with many missing pieces. Biomedica 2023; 43:288-311. [PMID: 37721899 PMCID: PMC10588969 DOI: 10.7705/biomedica.7052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/24/2023] [Indexed: 09/20/2023]
Abstract
Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.
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Wijayawardene NN, Boonyuen N, Ranaweera CB, de Zoysa HKS, Padmathilake RE, Nifla F, Dai DQ, Liu Y, Suwannarach N, Kumla J, Bamunuarachchige TC, Chen HH. OMICS and Other Advanced Technologies in Mycological Applications. J Fungi (Basel) 2023; 9:688. [PMID: 37367624 DOI: 10.3390/jof9060688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.
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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
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
- 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
| | - Nattawut Boonyuen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chathuranga B Ranaweera
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, General Sir John Kotelawala Defence University Sri Lanka, Kandawala Road, Rathmalana 10390, Sri Lanka
| | - Heethaka K S de Zoysa
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Rasanie E Padmathilake
- Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Pulliyankulama, Anuradhapura 50000, Sri Lanka
| | - Faarah Nifla
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Dong-Qin Dai
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Yanxia Liu
- Guizhou Academy of Tobacco Science, No.29, Longtanba Road, Guanshanhu District, Guiyang 550000, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thushara C Bamunuarachchige
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Huan-Huan Chen
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Agricultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Avasthi S, Gautam AK, Niranjan M, Verma RK, Karunarathna SC, Kumar A, Suwannarach N. Insights into Diversity, Distribution, and Systematics of Rust Genus Puccinia. J Fungi (Basel) 2023; 9:639. [PMID: 37367575 DOI: 10.3390/jof9060639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/21/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Puccinia, which comprises 4000 species, is the largest genus of rust fungi and one of the destructive plant pathogenic rust genera that are reported to infect both agricultural and nonagricultural plants with severe illnesses. The presence of bi-celled teliospores is one of the major features of these rust fungi that differentiated them from Uromyces, which is another largest genus of rust fungi. In the present study, an overview of the current knowledge on the general taxonomy and ecology of the rust genus Puccinia is presented. The status of the molecular identification of this genus along with updated species numbers and their current statuses in the 21st century are also presented, in addition to their threats to both agricultural and nonagricultural plants. Furthermore, a phylogenetic analysis based on ITS and LSU DNA sequence data available in GenBank and the published literature was performed to examine the intergeneric relationships of Puccinia. The obtained results revealed the worldwide distribution of Puccinia. Compared with other nations, a reasonable increase in research publications over the current century was demonstrated in Asian countries. The plant families Asteraceae and Poaceae were observed as the most infected in the 21st century. The phylogenetic studies of the LSU and ITS sequence data revealed the polyphyletic nature of Puccinia. In addition, the presences of too short, too lengthy, and incomplete sequences in the NCBI database demonstrate the need for extensive DNA-based analyses for a better understanding of the taxonomic placement of Puccinia.
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Affiliation(s)
- Shubhi Avasthi
- School of Studies in Botany, Jiwaji University, Gwalior 474011, India
| | - Ajay Kumar Gautam
- School of Agriculture, Abhilashi University, Mandi 175028, India
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar 249405, India
| | - Mekala Niranjan
- Department of Botany, Rajiv Gandhi University, Rono Hills, Doimukh, Itanagar 791112, India
- Fungal Biotechnology Lab, Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet 605014, India
| | - Rajnish Kumar Verma
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana 141004, India
| | - Samantha C Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- National Institute of Fundamental Studies (NIFS), Hantana Road, Kandy 20000, Sri Lanka
| | - Ashwani Kumar
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar 249405, India
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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Dos Reis JBA, Pappas Junior GJ, Lorenzi AS, Pinho DB, Costa AM, Bustamante MMDC, Vale HMMD. How Deep Can the Endophytic Mycobiome Go? A Case Study on Six Woody Species from the Brazilian Cerrado. J Fungi (Basel) 2023; 9:jof9050508. [PMID: 37233219 DOI: 10.3390/jof9050508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023] Open
Abstract
Elucidating the complex relationship between plants and endophytic fungi is very important in order to understand the maintenance of biodiversity, equity, stability, and ecosystem functioning. However, knowledge about the diversity of endophytic fungi from species of the native Brazilian Cerrado biome is poorly documented and remains largely unknown. These gaps led us to characterize the diversity of Cerrado endophytic foliar fungi associated with six woody species (Caryocar brasiliense, Dalbergia miscolobium, Leptolobium dasycarpum, Qualea parviflora, Ouratea hexasperma, and Styrax ferrugineus). Additionally, we investigated the influence of host plant identities on the structure of fungal communities. Culture-dependent methods coupled with DNA metabarcoding were employed. Irrespective of the approach, the phylum Ascomycota and the classes Dothideomycetes and Sordariomycetes were dominant. Using the cultivation-dependent method, 114 isolates were recovered from all the host species and classified into more than 20 genera and 50 species. Over 50 of the isolates belonged to the genus Diaporthe, and were distributed into more than 20 species. Metabarcoding revealed the phyla Chytridiomycota, Glomeromycota, Monoblepharomycota, Mortierellomycota, Olpidiomycota, Rozellomycota, and Zoopagomycota. These groups are reported for the first time as components of the endophytic mycobiome of Cerrado plant species. In total, 400 genera were found in all host species. A unique leaf endophytic mycobiome was identified in each host species, which differed not only by the distribution of fungal species, but also by the abundance of shared species. These findings highlight the importance of the Brazilian Cerrado as a reservoir of microbial species, and emphasize how endophytic fungal communities are diversified and adapted.
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Affiliation(s)
| | - Georgios Joannis Pappas Junior
- University of Brasília (UnB), Institute of Biological Sciences, Department of Cellular Biology, Brasília 70910-900, DF, Brazil
| | - Adriana Sturion Lorenzi
- University of Brasília (UnB), Institute of Biological Sciences, Department of Cellular Biology, Brasília 70910-900, DF, Brazil
| | - Danilo Batista Pinho
- University of Brasília (UnB), Institute of Biological Sciences, Department of Phytopathology, Brasília 70910-900, DF, Brazil
| | - Alexandra Martins Costa
- University of Brasília (UnB), Institute of Biological Sciences, Department of Ecology, Brasília 70910-900, DF, Brazil
| | | | - Helson Mario Martins do Vale
- University of Brasília (UnB), Institute of Biological Sciences, Department of Phytopathology, Brasília 70910-900, DF, Brazil
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Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N. Four principles to establish a universal virus taxonomy. PLoS Biol 2023; 21:e3001922. [PMID: 36780432 PMCID: PMC9925010 DOI: 10.1371/journal.pbio.3001922] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - F. Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Nicola G. A. Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences—BRTA, Derio, Spain
- Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz University, Poznan, Poland
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - W. Paul Duprex
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Valencia, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Maria Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Amy J. Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, United States of America
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alejandro Reyes-Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Stuart Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tim Skern
- Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, Arizona, United States of America
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Nikos Vasilakis
- Department of Pathology, Center of Vector-Borne and Zoonotic Diseases, Institute for Human Infection and Immunity and World Reference Center for Emerging Viruses and Arboviruses, The University of Texas Medical Branch, Galveston, Texas, United States of America
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Balkrishna A, Gautam AK, Avasthi S, Niranjan M, Verma RK, Arya V, Kumar A, Karunarathna SC, Suwannarach N. A Comprehensive Account of the Rust Genus Skierka ( Skierkaceae). J Fungi (Basel) 2022; 8:jof8121243. [PMID: 36547576 PMCID: PMC9784212 DOI: 10.3390/jof8121243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/10/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
The rust genus Skierka belonging to the phylum Basidiomycota was described in 1900 by Raciborski with Skierka canarii as the type species. The published literature on this rust genus reveals its ambiguity in taxonomic placement. It was challenging to taxonomically delineate and precisely identify each species within this genus due to the species sharing some common characteristics. The latest studies based on morphology taxonomy and molecular characteristics, however, have solved this puzzle now and placed this genus in its new family Skierkaceae. To understand all about the genus Skierka, this compilation was carried out to unveil the general characteristics, history, diversity, distribution, ecology, morphology and molecular taxonomy of different species of Skierka. After exploring 14 species of Skierka, it was observed that this genus is distributed in seven plant families in 19 countries all over the world. The genus appears to be well-represented in Asian and South American counties. This rust has not been reported from any European countries to date. The morpho-taxonomy of all species is well studied, but molecular analyses are still required. Only two species of the genus namely S. robusta and S. diploglottidis were identified based molecular analyses. Therefore, further studies should be focused on epitypifying the taxa that are too old and updating their taxonomy based on molecular, biochemical, and physiological aspects along with morphological characteristics. Multiple analytical methods should be considered when dealing with multi-locus datasets. This will increase our understanding of the diversity, distribution, and identification of these rust fungi.
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Affiliation(s)
- Acharya Balkrishna
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar 249405, India
- Department of Applied and Allied Sciences, University of Patanjali, Haridwar 249405, India
| | - Ajay Kumar Gautam
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar 249405, India
- Correspondence: (A.K.G.); (N.S.); Tel.: +91-7018321256 (A.K.G.); +66-86-5127518 (N.S.)
| | - Shubhi Avasthi
- School of Studies in Botany, Jiwaji University, Gwalior 474011, India
| | - Mekala Niranjan
- Department of Botany, Rajiv Gandhi University, Itanagar 791112, Arunachal Pradesh, India
| | - Rajnish Kumar Verma
- Mycology Lab., Department of Plant Pathology, Punjab Agricultural University, Ludhiana 141004, India
| | - Vedpriya Arya
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar 249405, India
- Department of Applied and Allied Sciences, University of Patanjali, Haridwar 249405, India
| | - Ashwani Kumar
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar 249405, India
| | - Samantha C. Karunarathna
- Center 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, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (A.K.G.); (N.S.); Tel.: +91-7018321256 (A.K.G.); +66-86-5127518 (N.S.)
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11
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Sydor M, Cofta G, Doczekalska B, Bonenberg A. Fungi in Mycelium-Based Composites: Usage and Recommendations. Materials (Basel) 2022; 15:ma15186283. [PMID: 36143594 PMCID: PMC9505859 DOI: 10.3390/ma15186283] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 05/13/2023]
Abstract
Mycelium-Based Composites (MBCs) are innovative engineering materials made from lignocellulosic by-products bonded with fungal mycelium. While some performance characteristics of MBCs are inferior to those of currently used engineering materials, these composites nevertheless prove to be superior in ecological aspects. Improving the properties of MBCs may be achieved using an adequate substrate type, fungus species, and manufacturing technology. This article presents scientifically verified guiding principles for choosing a fungus species to obtain the desired effect. This aim was realized based on analyses of scientific articles concerning MBCs, mycological literature, and patent documents. Based on these analyses, over 70 fungi species used to manufacture MBC have been identified and the most commonly used combinations of fungi species-substrate-manufacturing technology are presented. The main result of this review was to demonstrate the characteristics of the fungi considered optimal in terms of the resulting engineering material properties. Thus, a list of the 11 main fungus characteristics that increase the effectiveness in the engineering material formation include: rapid hyphae growth, high virulence, dimitic or trimitic hyphal system, white rot decay type, high versatility in nutrition, high tolerance to a substrate, environmental parameters, susceptibility to readily controlled factors, easy to deactivate, saprophytic, non-mycotoxic, and capability to biosynthesize natural active substances. An additional analysis result is a list of the names of fungus species, the types of substrates used, the applications of the material produced, and the main findings reported in the scientific literature.
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Affiliation(s)
- Maciej Sydor
- Department of Woodworking and Fundamentals of Machine Design, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, 60-637 Poznań, Poland
- Correspondence: ; Tel.: +48-618466144
| | - Grzegorz Cofta
- Department of Chemical Wood Technology, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, 60-637 Poznań, Poland
| | - Beata Doczekalska
- Department of Chemical Wood Technology, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, 60-637 Poznań, Poland
| | - Agata Bonenberg
- Institute of Interior Design and Industrial Design, Faculty of Architecture, Poznan University of Technology, 60-965 Poznań, Poland
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Oliveira M, Azevedo L. Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years. J Fungi (Basel) 2022; 8:803. [PMID: 36012792 PMCID: PMC9410331 DOI: 10.3390/jof8080803] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
Fungi are amongst the most abundant and diverse organisms. Despite being widely known for their adverse role in food spoilage or as pathogens for humans, animals, or plants, they also present several beneficial effects. Fungi contribute to human well-being due to their role as decomposers, degrading decay matter into smaller molecules which can be easily used by other ecosystem members. These organisms can produce medicinal compounds or modulate protective immune responses in human intestine. Fungi intervene in diverse food processes or act as a food supply. Due to fungal diversity, the unequivocal identification of these organisms is crucial to increasing their practical applications and decreasing their adverse effects. The process of identification could be achieved through the integral sequencing of fungi genomes. However, this procedure would be time-consuming and rather cost-inefficient. Therefore, several molecular markers have been developed to overcome these limitations. The chronology of DNA-based molecular markers development can be divided into three main steps: (1) prior to the development of the PCR technique (RFLP); (2) after the development of the PCR technique (RAPD, AFLP, ISSR, VNTR, SNP, InDels, and DNA barcoding); (3) after the development of the massive parallel sequencing technique (Metabarcoding and WGS). Therefore, the present review covers an overview of the most recently developed molecular markers used for fungal detection and identification.
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Li J, Wu H, Li Y, Li X, Song J, Suwannarach N, Wijayawardene NN. Taxonomy, Phylogenetic and Ancestral Area Reconstruction in Phyllachora, with Four Novel Species from Northwestern China. J Fungi (Basel) 2022; 8:520. [PMID: 35628775 PMCID: PMC9144558 DOI: 10.3390/jof8050520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 02/04/2023] Open
Abstract
The members of Phyllachora are biotrophic, obligate plant parasitic fungi featuring a high degree of host specificity. This genus also features a high degree of species richness and worldwide distribution. In this study, four species occurring on leaf and stem of two different species of grass were collected from Shanxi and Shaanxi Provinces, China. Based on morphological analysis, multigene (combined data set of LSU, SSU, and ITS) phylogenetic analyses (maximum likelihood and Bayesian analysis), and host relationship, we introduce herein four new taxa of Phyllachora. Ancestral area reconstruction analysis showed that the ancestral area of Phyllachora occurred in Latin America about 194 Mya. Novel taxa are compared with the related Phyllachora species. Detailed descriptions, illustrations, and notes are provided for each species.
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