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Stallman JK, Johnston PR, Lickey EB, Marlin M, Melie T, Quandt CA, Aime MC, Haelewaters D. Recent fieldwork and fungarium studies double known diversity of Chlorosplenium and improve understanding of species distributions. Mycologia 2024:1-26. [PMID: 39141581 DOI: 10.1080/00275514.2024.2364567] [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: 01/21/2024] [Accepted: 06/03/2024] [Indexed: 08/16/2024]
Abstract
Chlorosplenium is a small genus comprising five species of inoperculate discomycetes in the order Helotiales (Leotiomycetes) often recognizable by their bright yellowish-green colors and gregarious growth on wood. In this study, we describe five new species-C. aotearoa, C. australiense, C. cusucoense, C. epimorsicum, and C. hawaiiense-based on a combination of recent fieldwork and examination of previously collected fungarium specimens. We use an integrative taxonomic approach to support the distinction of new species, incorporating morphology and DNA sequence data with biogeography. Macro- and micromorphological features of apothecia for all species and culture characteristics for four of the five new species are documented. A multilocus phylogeny based on nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2, partial large subunit nuc ribosomal DNA (28S nuc rDNA), and A-B regions of the largest subunit of RNA polymerase II (RPB1) gene is presented. Additionally, we report Chlorosplenium chlora from Europe for the first time and expand our knowledge of the diversity and distributions of species in this genus in America, Australia, and New Zealand.
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Affiliation(s)
- Jeffery K Stallman
- Department of Botany and Plant Pathology, Purdue University, Lafayette, Indiana 47901
| | | | - Edgar B Lickey
- Department of Biology and Environmental Science, Bridgewater College, Bridgewater, Virginia 22812
| | - Maria Marlin
- Department of Biology and Environmental Science, Bridgewater College, Bridgewater, Virginia 22812
| | - Tina Melie
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, Lafayette, Indiana 47901
| | - Danny Haelewaters
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309
- Research Group Mycology, Department of Biology, Ghent University, 9000 Ghent, Belgium
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
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2
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Miranda FM, Azevedo VC, Ramos RJ, Renard BY, Piro VC. Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2. BMC Bioinformatics 2024; 25:228. [PMID: 38956506 PMCID: PMC11220968 DOI: 10.1186/s12859-024-05839-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/11/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be beneficial when administered as probiotics. In mycology, the internal transcribed spacer (ITS) region was adopted as the universal marker for classifying fungi. Hence, an accurate and robust method for ITS classification is not only desired for the purpose of better diversity estimation, but it can also help us gain a deeper insight into the dynamics of environmental communities and ultimately comprehend whether the abundance of certain species correlate with health and disease. Although many methods have been proposed for taxonomic classification, to the best of our knowledge, none of them fully explore the taxonomic tree hierarchy when building their models. This in turn, leads to lower generalization power and higher risk of committing classification errors. RESULTS Here we introduce HiTaC, a robust hierarchical machine learning model for accurate ITS classification, which requires a small amount of data for training and can handle imbalanced datasets. HiTaC was thoroughly evaluated with the established TAXXI benchmark and could correctly classify fungal ITS sequences of varying lengths and a range of identity differences between the training and test data. HiTaC outperforms state-of-the-art methods when trained over noisy data, consistently achieving higher F1-score and sensitivity across different taxonomic ranks, improving sensitivity by 6.9 percentage points over top methods in the most noisy dataset available on TAXXI. CONCLUSIONS HiTaC is publicly available at the Python package index, BIOCONDA and Docker Hub. It is released under the new BSD license, allowing free use in academia and industry. Source code and documentation, which includes installation and usage instructions, are available at https://gitlab.com/dacs-hpi/hitac .
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Affiliation(s)
- Fábio M Miranda
- Data Analytics and Computational Statistics, Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Vasco C Azevedo
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rommel J Ramos
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Centro de Computação de Alto Desempenho, Universidade Federal do Pará, Belém, Brazil
| | - Bernhard Y Renard
- Data Analytics and Computational Statistics, Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | - Vitor C Piro
- Data Analytics and Computational Statistics, Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
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Zhang R, Chen Y, Wang W, Chen J, Liu D, Zhang L, Xiang Q, Zhao K, Ma M, Yu X, Chen Q, Penttinen P, Gu Y. Combined transcriptomic and metabolomic analysis revealed that pH changes affected the expression of carbohydrate and ribosome biogenesis-related genes in Aspergillus niger SICU-33. Front Microbiol 2024; 15:1389268. [PMID: 38962137 PMCID: PMC11220263 DOI: 10.3389/fmicb.2024.1389268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/03/2024] [Indexed: 07/05/2024] Open
Abstract
The process of carbohydrate metabolism and genetic information transfer is an important part of the study on the effects of the external environment on microbial growth and development. As one of the most significant environmental parameters, pH has an important effect on mycelial growth. In this study, the effects of environmental pH on the growth and nutrient composition of Aspergillus niger (A. niger) filaments were determined. The pH values of the medium were 5, 7, and 9, respectively, and the molecular mechanism was further investigated by transcriptomics and metabolomics methods. The results showed that pH 5 and 9 significantly inhibited filament growth and polysaccharide accumulation of A. niger. Further, the mycelium biomass of A. niger and the crude polysaccharide content was higher when the medium's pH was 7. The DEGs related to ribosome biogenesis were the most abundant, and the downregulated expression of genes encoding XRN1, RRM, and RIO1 affected protein translation, modification, and carbohydrate metabolism in fungi. The dynamic changes of pargyline and choline were in response to the oxidative metabolism of A. niger SICU-33. The ribophorin_I enzymes and DL-lactate may be important substances related to pH changes during carbohydrate metabolism of A.niger SICU-33. The results of this study provide useful transcriptomic and metabolomic information for further analyzing the bioinformatic characteristics of A. niger and improving the application in ecological agricultural fermentation.
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Affiliation(s)
- Runji Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yulan Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Wenxian Wang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Juan Chen
- Liangshan Tobacco Corporation of Sichuan Province, Xichang, China
| | - Dongyang Liu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Liangshan Tobacco Corporation of Sichuan Province, Xichang, China
| | - Lingzi Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Quanju Xiang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Menggen Ma
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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Tennakoon DS, Thambugala KM, de Silva NI, Song HY, Suwannarach N, Chen FS, Hu DM. An overview of Melanommataceae (Pleosporales, Dothideomycetes): Current insight into the host associations and geographical distribution with some interesting novel additions from plant litter. MycoKeys 2024; 106:43-96. [PMID: 38919541 PMCID: PMC11196893 DOI: 10.3897/mycokeys.106.125044] [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: 04/09/2024] [Accepted: 05/19/2024] [Indexed: 06/27/2024] Open
Abstract
Melanommataceous species exhibit high diversity with a cosmopolitan distribution worldwide and show a prominent saprobic lifestyle. In this study, we explored five saprobic species collected from plant litter substrates from terrestrial habitats in China and Thailand. A combination of morphological characteristics and multi-locus phylogenetic analyses was used to determine their taxonomic classifications. Maximum Likelihood and Bayesian Inference analyses of combined LSU, SSU, ITS and tef1-α sequence data were used to clarify the phylogenetic affinities of the species. Byssosphaeriapoaceicola and Herpotrichiazingiberacearum are introduced as new species, while three new host records, Bertiellafici, By.siamensis and Melanommapopulicola are also reported from litter of Cinnamomumverum, Citrustrifoliata and Fagussylvatica, respectively. Yet, despite the rising interest in the melanommataceous species, there is a considerable gap in knowledge on their host associations and geographical distributions. Consequently, we compiled the host-species associations and geographical distributions of all the so far known melanommataceous species.
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Affiliation(s)
- Danushka S. Tennakoon
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China
| | - Kasun M. Thambugala
- Nanchang Key Laboratory of Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China
| | - Nimali I. de Silva
- Jiangxi Provincial Key Laboratory of Subtropical Forest Resource Cultivation, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hai-Yan Song
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China
| | - Nakarin Suwannarach
- Jiangxi Provincial Key Laboratory of Subtropical Forest Resource Cultivation, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fu-Sheng Chen
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China
| | - Dian-Ming Hu
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang 330045, China
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Al Qutaibi M, Kagne SR. Exploring the Phytochemical Compositions, Antioxidant Activity, and Nutritional Potentials of Edible and Medicinal Mushrooms. Int J Microbiol 2024; 2024:6660423. [PMID: 38841191 PMCID: PMC11152763 DOI: 10.1155/2024/6660423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 03/22/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024] Open
Abstract
Mushrooms are a valuable source of food and medicine that have been used for centuries in various cultures. They contain a variety of phytochemicals, such as terpenoids and polysaccharides, that exhibit diverse biological activities, such as antioxidant, anti-inflammatory, anticancer, antimicrobial, immunomodulatory, and antidiabetic effects. However, mushroom's phytochemical composition and bioactivity vary depending on their species, cultivation conditions, processing methods, and extraction techniques. Therefore, using reliable analytical methods and standardized protocols is important for systematically evaluating the quality and quantity of mushroom phytochemicals and their therapeutic potential. This review provides a bibliometric analysis of the recent literature on biological activities, highlights trends in the field, and highlights the countries and journals with the highest contribution. It also discusses the nutritional value of the total content of phenolic and other phytochemicals in some species of mushrooms.
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Affiliation(s)
- Mohammed Al Qutaibi
- Department of Medical Microbiology, Faculty of Science, Ibb University, Ibb, Yemen
- Department of Microbiology, Badrinarayan Barwale College, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad 431001, India
| | - Suresh R. Kagne
- Department of Microbiology, Badrinarayan Barwale College, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad 431001, India
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Morgado DS, Castro R, Ribeiro-Alves M, Corrêa-Moreira D, Silva JCADLE, Menezes RC, Oliveira MME. Systematic review of literature to evaluate global distribution of species of the Sporothrix genus stored in culture collections. Front Cell Infect Microbiol 2024; 14:1382508. [PMID: 38828263 PMCID: PMC11140055 DOI: 10.3389/fcimb.2024.1382508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/17/2024] [Indexed: 06/05/2024] Open
Abstract
Introduction Sporotrichosis is a subcutaneous mycosis caused by fungi of the genus Sporothrix sp. Phenotypic and genotypic differences have been associated with their geographic distribution, virulence, or clinical manifestation of sporotrichosis. In the past decade, the interest in identifying species of the Sporothrix sp. has been increasing, due to its epidemiological importance and, in consequence, is important to know how to preserve them for future studies, in culture collection. Aims The purposes of this study were to analyze the global distribution of environmental isolates and/or causal agents of sporotrichosis identified by polyphasic taxonomy, with mandatory use of molecular identification, and to evaluate the percentages and distribution of isolates stored in culture collections. Methods A systematic review of articles on animal and human sporotrichosis and/or environmental isolation of the fungus, from 2007 to 2023, was done. Results: Our results demonstrated that, S. globosa, S. schenckii, and S. brasiliensis were the most identified species. With respect to the deposit and maintenance of species, we observed that only 17% of the strains of Sporothrix sp. isolated in the world are preserved in a culture collection. Conclusions This systematic review confirmed a difficulty in obtaining the frequency of Sporothrix species stored in culture collection and insufficient data on the molecular identification mainly of animal sporotrichosis and isolation of Sporothrix sp. in environmental samples.
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Affiliation(s)
- Debora Salgado Morgado
- Laboratory of Taxonomy, Biochemistry and Bioprospecting of Fungi, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Rodolfo Castro
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- Institute of Collective Health, Federal University of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo Ribeiro-Alves
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Danielly Corrêa-Moreira
- Laboratory of Taxonomy, Biochemistry and Bioprospecting of Fungi, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Rodrigo Caldas Menezes
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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Phookamsak R, Hongsanan S, Bhat DJ, Wanasinghe DN, Promputtha I, Suwannarach N, Kumla J, Xie N, Dawoud TM, Mortimer PE, Xu J, Lumyong S. Exploring ascomycete diversity in Yunnan II: Introducing three novel species in the suborder Massarineae (Dothideomycetes, Pleosporales) from fern and grasses. MycoKeys 2024; 104:9-50. [PMID: 38665970 PMCID: PMC11040200 DOI: 10.3897/mycokeys.104.112149] [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: 09/04/2023] [Accepted: 10/09/2023] [Indexed: 04/28/2024] Open
Abstract
This article presents the results of an ongoing inventory of Ascomycota in Yunnan, China, carried out as part of the research project series "Exploring ascomycete diversity in Yunnan". From over 100 samples collected from diverse host substrates, microfungi have been isolated, identified and are currently being documented. The primary objective of this research is to promote the discovery of novel taxa and explore the ascomycete diversity in the region, utilising a morphology-phylogeny approach. This article represents the second series of species descriptions for the project and introduces three undocumented species found in the families Bambusicolaceae, Dictyosporiaceae and Periconiaceae, belonging to the suborder Massarineae (Pleosporales, Dothideomycetes). These novel taxa exhibit typical morphological characteristics of Bambusicola, Periconia and Trichobotrys, leading to their designation as Bambusicolahongheensis, Periconiakunmingensis and Trichobotryssinensis. Comprehensive multigene phylogenetic analyses were conducted to validate the novelty of these species. The results revealed well-defined clades that are clearly distinct from other related species, providing robust support for their placement within their respective families. Notably, this study unveils the phylogenetic affinity of Trichobotrys within Dictyosporiaceae for the first time. Additionally, the synanamorphism for the genus Trichobotrys is also reported for the first time. Detailed descriptions, illustrations and updated phylogenies of the novel species are provided, and thus presenting a valuable resource for researchers and mycologists interested in the diversity of ascomycetes in Yunnan. By enhancing our understanding of the Ascomycota diversity in this region, this research contributes to the broader field of fungal taxonomy and their phylogenetic understanding.
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Affiliation(s)
- Rungtiwa Phookamsak
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
- Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe, 654400, Yunnan Province, China
| | - Sinang Hongsanan
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Darbhe Jayarama Bhat
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Vishnugupta Vishwavidyapeetam, Ashoke, Gokarna 581326, India
| | - Dhanushka N. Wanasinghe
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
- Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe, 654400, Yunnan Province, China
- CIFOR-ICRAF China Program, World Agroforestry (ICRAF), Kunming 650201, Yunnan Province, China
- Center for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
| | - Itthayakorn Promputtha
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nakarin Suwannarach
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Ning Xie
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Turki M. Dawoud
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Peter E. Mortimer
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
- Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe, 654400, Yunnan Province, China
| | - Jianchu Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
- Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe, 654400, Yunnan Province, China
- CIFOR-ICRAF China Program, World Agroforestry (ICRAF), Kunming 650201, Yunnan Province, China
| | - Saisamorn Lumyong
- Center of Excellence in 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 Santos VHP, Andre RS, Dos Anjos JP, Mercante LA, Correa DS, Silva EO. Biotransformation of progesterone by endophytic fungal cells immobilized on electrospun nanofibrous membrane. Folia Microbiol (Praha) 2024; 69:407-414. [PMID: 37979123 DOI: 10.1007/s12223-023-01113-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Biotransformation of steroids by fungi has been raised as a successful, eco-friendly, and cost-effective biotechnological alternative for chemical derivatization. Endophytic fungi live inside vegetal tissues without causing damage to the host plant, making available unique enzymes that carry out uncommon reactions. Moreover, using nanofibrous membranes as support for immobilizing fungal cells is a powerful strategy to improve their performance by enabling the combined action of adsorption and transformation processes, along with increasing the stability of the fungal cell. In the present study, we report the use of polyacrylonitrile nanofibrous membrane (PAN NFM) produced by electrospinning as supporting material for immobilizing the endophytic fungus Penicillium citrinum H7 aiming the biotransformation of progesterone. The PAN@H7 NFM displayed a high progesterone transformation efficiency (above 90%). The investigation of the biotransformation pathway of progesterone allowed the putative structural characterization of its main fungal metabolite by GC-MS analysis. The oxidative potential of P. citrinum H7 was selective for the C-17 position of the steroidal nucleus.
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Affiliation(s)
| | - Rafaela S Andre
- Nanotechnology National Laboratory for Agriculture (LNNA), Embrapa Instrumentation, São Carlos, 13560-970, Brazil
| | - Jeancarlo Pereira Dos Anjos
- University Center SENAI CIMATEC, Salvador, 41650-010, Brazil
- INCT in Energy and Environment, Federal University of Bahia, Salvador, 40170-115, Brazil
| | - Luiza A Mercante
- Institute of Chemistry, Federal University of Bahia, Salvador, 40170-115, Brazil
| | - Daniel S Correa
- Nanotechnology National Laboratory for Agriculture (LNNA), Embrapa Instrumentation, São Carlos, 13560-970, Brazil
| | - Eliane Oliveira Silva
- Department of Organic Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, 40170-115, Brazil.
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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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Man BY, Xiang X, Cheng XY, Wang HM, Su CT, Huang QB, Luo Y, Zhang C, Cheng G, Ni YY, Shao XH. Deconstructing the Dimensions of Mycobiome Fingerprints in Luohandu Cave, Guilin, Southern China. Microorganisms 2024; 12:211. [PMID: 38276196 PMCID: PMC10818497 DOI: 10.3390/microorganisms12010211] [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: 12/12/2023] [Revised: 01/14/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Subterranean karst caves are windows into the terrestrial subsurface to deconstruct the dimensions of mycobiome fingerprints. However, impeded by the constraints of remote locations, the inaccessibility of specimens and technical limitations, the mycobiome of subterranean karst caves has remained largely unknown. Weathered rock and sediment samples were collected from Luohandu cave (Guilin, Southern China) and subjected to Illumina Hiseq sequencing of ITS1 genes. A total of 267 known genera and 90 known orders in 15 phyla were revealed in the mycobiomes. Ascomycota dominated all samples, followed by Basidiomycota and Mortierellomycota. The sediments possessed the relatively highest alpha diversity and were significantly different from weathered rocks according to the diversity indices and richness metrics. Fifteen families and eight genera with significant differences were detected in the sediment samples. The Ca/Mg ratio appeared to significantly affect the structure of the mycobiome communities. Ascomycota appeared to exert a controlling influence on the mycobiome co-occurrence network of the sediments, while Ascomycota and Basidiomycota were found to be the main phyla in the mycobiome co-occurrence network of weathered rocks. Our results provide a more comprehensive dimension to the mycobiome fingerprints of Luohandu cave and a new window into the mycobiome communities and the ecology of subterranean karst cave ecosystems.
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Affiliation(s)
- Bai-Ying Man
- College of Life Science, Shangrao Normal University, Shangrao 334001, China; (X.X.); (Y.L.); (C.Z.); (G.C.); (Y.-Y.N.); (X.-H.S.)
- Key Laboratory for Regional Plants Conservation and Ecological Restoration of Northeast Jiangxi, Shangrao Normal University, Shangrao 334001, China
| | - Xing Xiang
- College of Life Science, Shangrao Normal University, Shangrao 334001, China; (X.X.); (Y.L.); (C.Z.); (G.C.); (Y.-Y.N.); (X.-H.S.)
- Key Laboratory for Regional Plants Conservation and Ecological Restoration of Northeast Jiangxi, Shangrao Normal University, Shangrao 334001, China
| | - Xiao-Yu Cheng
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China;
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hong-Mei Wang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China;
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Chun-Tian Su
- Institute of Karst Geology, CAGS/Key Laboratory of Karst Dynamics, MNR & GZAR, Guilin 541004, Guangxi, China; (C.-T.S.); (Q.-B.H.)
- Pingguo Guangxi, Karst Ecosystem, National Observation and Research Station, Pingguo 531406, Guangxi, China
| | - Qi-Bo Huang
- Institute of Karst Geology, CAGS/Key Laboratory of Karst Dynamics, MNR & GZAR, Guilin 541004, Guangxi, China; (C.-T.S.); (Q.-B.H.)
- Pingguo Guangxi, Karst Ecosystem, National Observation and Research Station, Pingguo 531406, Guangxi, China
| | - Yang Luo
- College of Life Science, Shangrao Normal University, Shangrao 334001, China; (X.X.); (Y.L.); (C.Z.); (G.C.); (Y.-Y.N.); (X.-H.S.)
- Key Laboratory for Regional Plants Conservation and Ecological Restoration of Northeast Jiangxi, Shangrao Normal University, Shangrao 334001, China
| | - Chao Zhang
- College of Life Science, Shangrao Normal University, Shangrao 334001, China; (X.X.); (Y.L.); (C.Z.); (G.C.); (Y.-Y.N.); (X.-H.S.)
- Key Laboratory for Regional Plants Conservation and Ecological Restoration of Northeast Jiangxi, Shangrao Normal University, Shangrao 334001, China
| | - Gang Cheng
- College of Life Science, Shangrao Normal University, Shangrao 334001, China; (X.X.); (Y.L.); (C.Z.); (G.C.); (Y.-Y.N.); (X.-H.S.)
- Key Laboratory for Regional Plants Conservation and Ecological Restoration of Northeast Jiangxi, Shangrao Normal University, Shangrao 334001, China
| | - Yu-Yang Ni
- College of Life Science, Shangrao Normal University, Shangrao 334001, China; (X.X.); (Y.L.); (C.Z.); (G.C.); (Y.-Y.N.); (X.-H.S.)
- Key Laboratory for Regional Plants Conservation and Ecological Restoration of Northeast Jiangxi, Shangrao Normal University, Shangrao 334001, China
| | - Xing-Hua Shao
- College of Life Science, Shangrao Normal University, Shangrao 334001, China; (X.X.); (Y.L.); (C.Z.); (G.C.); (Y.-Y.N.); (X.-H.S.)
- Key Laboratory for Regional Plants Conservation and Ecological Restoration of Northeast Jiangxi, Shangrao Normal University, Shangrao 334001, China
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11
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Waqar S, Bhat AA, Khan AA. Endophytic fungi: Unravelling plant-endophyte interaction and the multifaceted role of fungal endophytes in stress amelioration. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108174. [PMID: 38070242 DOI: 10.1016/j.plaphy.2023.108174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 02/15/2024]
Abstract
Endophytic fungi colonize interior plant tissue and mostly form mutualistic associations with their host plant. Plant-endophyte interaction is a complex mechanism and is currently a focus of research to understand the underlying mechanism of endophyte asymptomatic colonization, the process of evading plant immune response, modulation of gene expression, and establishment of a balanced mutualistic relationship. Fungal endophytes rely on plant hosts for nutrients, shelter, and transmission and improve the host plant's tolerance against biotic stresses, including -herbivores, nematodes, bacterial, fungal, viral, nematode, and other phytopathogens. Endophytic fungi have been reported to improve plant health by reducing and eradicating the harmful effect of phytopathogens through competition for space or nutrients, mycoparasitism, and through direct or indirect defense systems by producing secondary metabolites as well as by induced systemic resistance (ISR). Additionally, for efficient crop improvement, practicing them would be a fruitful step for a sustainable approach. This review article summarizes the current research progress in plant-endophyte interaction and the fungal endophyte mechanism to overcome host defense responses, their subsequent colonization, and the establishment of a balanced mutualistic interaction with host plants. This review also highlighted the potential of fungal endophytes in the amelioration of biotic stress. We have also discussed the relevance of various bioactive compounds possessing antimicrobial potential against a variety of agricultural pathogens. Furthermore, endophyte-mediated ISR is also emphasized.
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Affiliation(s)
- Sonia Waqar
- Section of Environmental Botany and Plant Pathology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.
| | - Adil Ameen Bhat
- Section of Environmental Botany and Plant Pathology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.
| | - Abrar Ahmad Khan
- Section of Environmental Botany and Plant Pathology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.
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12
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Nandi S, Sikder R, Rapior S, Arnould S, Simal-Gandara J, Acharya K. A review for cancer treatment with mushroom metabolites through targeting mitochondrial signaling pathway: In vitro and in vivo evaluations, clinical studies and future prospects for mycomedicine. Fitoterapia 2024; 172:105681. [PMID: 37743029 DOI: 10.1016/j.fitote.2023.105681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Resistance to apoptosis stands as a roadblock to the successful pharmacological execution of anticancer drug effect. A comprehensive insight into apoptotic signaling pathways and an understanding of the mechanisms of apoptosis resistance are crucial to unveil new drug targets. At this juncture, researchers are heading towards natural sources in particular, mushroom as their potential drugs leads to being the reliable source of potent bioactive compounds. Given the continuous increase in cancer cases, the potent anticancer efficacy of mushrooms has inevitably become a fascinating object to researchers due to their higher safety margin and multitarget. This review aimed to collect and summarize all the available scientific data on mushrooms from their extracts to bioactive molecules in order to suggest their anticancer attributes via a mitochondrion -mediated intrinsic signaling mechanism. Compiled data revealed that bioactive components of mushrooms including polysaccharides, sterols and terpenoids as well as extracts prepared using 15 different solvents from 53 species could be effective in the supportive treatment of 20 various cancers. The underlying therapeutic mechanisms of the studied mushrooms are explored in this review through diverse and complementary investigations: in vitro assays, pre-clinical studies and clinical randomized controlled trials. The processes mainly involved were ROS production, mitochondrial membrane dysfunction, and action of caspase 3, caspase 9, XIAP, cIAP, p53, Bax, and Bcl-2. In summary, the study provides facts pertaining to the potential beneficial effect of mushroom extracts and their active compounds against various types of cancer and is shedding light on the underlying targeted signaling pathways.
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Affiliation(s)
- Sudeshna Nandi
- Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, WB 700019, India
| | - Rimpa Sikder
- Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, WB 700019, India
| | - Sylvie Rapior
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Laboratory of Botany, Phytochemistry and Mycology, Faculty of Pharmacy, 15 Avenue Charles Flahault, 34093 Montpellier, France
| | - Stéphanie Arnould
- Centre for Integrative Biology, Molecular, Cellular & Developmental biology unit, CNRS UMR 5077, Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France
| | - Jesus Simal-Gandara
- Universidade de Vigo, Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, E-32004 Ourense, Spain.
| | - Krishnendu Acharya
- Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, WB 700019, India.
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13
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Dutra YLG, Rosado AWC, Condé TO, Leão AF, Neves SDC, Fraga LMS, Kasuya MCM, Pereira OL. Two new Cladosporium species from a quartzite cave in Brazil. Braz J Microbiol 2023; 54:3021-3031. [PMID: 37880564 PMCID: PMC10689331 DOI: 10.1007/s42770-023-01156-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
Caves are underground and natural environments mainly found in rocky terrain. Caves have a very specific microclimate, which benefits the occurrence of specific fungi. In recent studies, researchers have observed that caves harbour a great diversity of fungi. However, studies on fungal diversity in Brazilian caves are still incipient. In September 2019, airborne spore and soil samples were collected from the Monte Cristo cave, in the Southern Espinhaço Range, Diamantina, Minas Gerais state, Brazil. Two Cladosporium single-spore isolates, among other genera, were obtained from these samples. This study aimed to characterise these two fungal isolates based on their DNA sequence data and morphology. Phylogenetic analyses of the rDNA-ITS, ACT and TEF1-α loci revealed that the isolates belonged to the Cladosporium cladosporioides species complex. Both isolates did not cluster with any known species and were formally described and named herein as C. diamantinense and C. speluncae. This study presents taxonomic novelties and contributes to the knowledge about the fungal diversity in Brazilian caves.
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Affiliation(s)
- Yan Lucas Gomes Dutra
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - André Wilson Campos Rosado
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Thiago Oliveira Condé
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Ana Flávia Leão
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Soraya de Carvalho Neves
- Instituto de Ciência e Tecnologia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, 39100-000, Brazil
| | - Lucio Mauro Soares Fraga
- Instituto de Ciência e Tecnologia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, 39100-000, Brazil
| | | | - Olinto Liparini Pereira
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil.
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil.
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14
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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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15
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Abel-Fernández E, Fernández-Caldas E. Allergy to fungi: Advances in the understanding of fungal allergens. Mol Immunol 2023; 163:216-223. [PMID: 37864931 DOI: 10.1016/j.molimm.2023.09.017] [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: 05/23/2023] [Revised: 09/20/2023] [Accepted: 09/29/2023] [Indexed: 10/23/2023]
Abstract
Allergic diseases are a major health problem due to their increasing incidence and high prevalence worldwide. Asthma has several aetiologies, and allergy plays an important role in its development in approximately 60% of adults and 80% of children and adolescents. Although the link between aeroallergen sensitization and asthma exacerbations has been long recognized, the investigations of the triggering allergens may be superficial in many asthma cases. The main allergenic sources related to asthma, and other allergic diseases, are pollens, mites, fungi, and animal epithelia. Fungi are considered the third most frequent cause of respiratory pathologies. Asthma caused by several fungi species may have a bad prognosis in some cases due to its severity and difficulty in avoidance methods. Despite the recognised relevance of fungi in respiratory allergies, the knowledge about fungal allergens seems to be scarce, with few descriptions of new allergens, compared to other allergenic sources. The study of major, minor, and cross-reactive fungal allergens, and their relevance in the allergic disease, might be crucial, not only to accurately diagnose these allergies, but also to predict exacerbations and responses to therapies, as well as for the development of personalized treatment plans in a fast-changing climate scenario.
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16
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Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. MICROBIOME RESEARCH REPORTS 2023; 3:2. [PMID: 38455081 PMCID: PMC10917621 DOI: 10.20517/mrr.2023.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 03/09/2024]
Abstract
Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.
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Affiliation(s)
| | | | | | - Duccio Cavalieri
- Correspondence to: Prof. Duccio Cavalieri, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy. E-mail:
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17
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Pagani DM, Ventura SPR, Vu D, Mendes-Pereira T, Ribeiro Tomé LM, de Carvalho DS, Costa-Rezende DH, Kato RB, García GJY, Geml J, Robert V, They NH, Brenig B, Azevedo V, Scroferneker ML, Valente P, Góes-Neto A. Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon. J Fungi (Basel) 2023; 9:890. [PMID: 37754998 PMCID: PMC10532596 DOI: 10.3390/jof9090890] [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: 07/25/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota.
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Affiliation(s)
- Danielle Machado Pagani
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil; (D.M.P.); (P.V.)
| | - Stefânia P. R. Ventura
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (D.V.); (V.R.)
| | - Thairine Mendes-Pereira
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Luiz Marcelo Ribeiro Tomé
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Daniel Santana de Carvalho
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Diogo Henrique Costa-Rezende
- Departamento de Ciências Biológicas, Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, BA, Brazil;
| | - Rodrigo Bentes Kato
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - Glen Jasper Yupanqui García
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - József Geml
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Leányka U. 6, 3300 Eger, Hungary;
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (D.V.); (V.R.)
| | - Ng Haig They
- Laboratório de Ecologia Aquática Microbiana, Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Departamento Interdisciplinar, Centro de Estudos Costeiros, Limnológicos e Marinhos, Universidade Federal do Rio Grande do Sul, Campus Litoral Norte, Tramandaí 95590-000, RS, Brazil;
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Goettingen, 37073 Göttingen, Germany;
| | - Vasco Azevedo
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
- Laboratory of Cellular and Molecular Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Maria Lúcia Scroferneker
- Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil;
| | - Patricia Valente
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil; (D.M.P.); (P.V.)
| | - Aristóteles Góes-Neto
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
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18
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Abel-Fernández E, Martínez MJ, Galán T, Pineda F. Going over Fungal Allergy: Alternaria alternata and Its Allergens. J Fungi (Basel) 2023; 9:jof9050582. [PMID: 37233293 DOI: 10.3390/jof9050582] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Fungal allergy is the third most frequent cause of respiratory pathologies and the most related to a poor prognosis of asthma. The genera Alternaria and Cladosporium are the most frequently associated with allergic respiratory diseases, with Alternaria being the one with the highest prevalence of sensitization. Alternaria alternata is an outdoor fungus whose spores disseminate in warm and dry air, reaching peak levels in temperate summers. Alternaria can also be found in damp and insufficiently ventilated houses, causing what is known as sick building syndrome. Thus, exposure to fungal allergens can occur outdoors and indoors. However, not only spores but also fungal fragments contain detectable amounts of allergens and may function as aeroallergenic sources. Allergenic extracts of Alternaria hyphae and spores are still in use for the diagnosis and treatment of allergic diseases but are variable and insufficiently standardised, as they are often a random mixture of allergenic ingredients and casual impurities. Thus, diagnosis of fungal allergy has been difficult, and knowledge about new fungal allergens is stuck. The number of allergens described in Fungi remains almost constant while new allergens are being found in the Plantae and Animalia kingdoms. Given Alt a 1 is not the unique Alternaria allergen eliciting allergy symptoms, component-resolved diagnosis strategies should be applied to diagnose fungal allergy. To date, twelve A. alternata allergens are accepted in the WHO/IUIS Allergen Nomenclature Subcommittee, many of them are enzymes: Alt a 4 (disulfide isomerase), Alt a 6 (enolase), Alt a 8 (mannitol de-hydrogenase), Alt a 10 (aldehyde dehydrogenase), Alt a 13 (glutathione-S-transferase) and Alt a MnSOD (Mn superoxide dismutase), and others have structural and regulatory functions such as Alt a 5 and Alt a 12, Alt a 3, Alt a 7. The function of Alt a 1 and Alt a 9 remains unknown. Other four allergens are included in other medical databases (e.g., Allergome): Alt a NTF2, Alt a TCTP, and Alt a 70 kDa. Despite Alt a 1 being the A. alternata major allergen, other allergens, such as enolase, Alt a 6 or MnSOD, Alt a 14 have been suggested to be included in the diagnosis panel of fungal allergy.
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Affiliation(s)
- Eva Abel-Fernández
- Applied Science, Inmunotek S.L., Parque Científico Tecnológico Alcalá de Henares, 28805 Madrid, Spain
| | - María José Martínez
- Applied Science, Inmunotek S.L., Parque Científico Tecnológico Alcalá de Henares, 28805 Madrid, Spain
| | - Tania Galán
- Applied Science, Inmunotek S.L., Parque Científico Tecnológico Alcalá de Henares, 28805 Madrid, Spain
| | - Fernando Pineda
- Applied Science, Inmunotek S.L., Parque Científico Tecnológico Alcalá de Henares, 28805 Madrid, Spain
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Tang D, Huang O, Zou W, Wang Y, Wang Y, Dong Q, Sun T, Yang G, Yu H. Six new species of zombie-ant fungi from Yunnan in China. IMA Fungus 2023; 14:9. [PMID: 37170179 PMCID: PMC10173673 DOI: 10.1186/s43008-023-00114-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 03/28/2023] [Indexed: 05/13/2023] Open
Abstract
Some Ophiocordyceps species infecting ants are able to manipulate the host behavior. The hosts are manipulated in order to move to location that are advantageous for fungal spore transmission. Ophiocordyceps species that are able to manipulate the ant's behavior are called "zombie-ant fungi". They are widespread within tropical forests worldwide, with relatively few reports from subtropical monsoon evergreen broad-leaf forest. Zombie-ant fungi have been described and reported in different countries worldwide. However, there were a few reports from China. This study proposed six new species of zombie-ant fungi from China based on multi-gene (SSU, LSU, TEF, RPB1 and RPB2) phylogenetic analyses and morphological characteristics. Six novel species of Ophiocordyceps from China were identified as the Ophiocordyceps unilateralis core clade, forming a separate lineage with other species. Six novel species of Ophiocordyceps with hirsutella-like asexual morphs exclusively infecting ants were presented herein, namely, Ophiocordyceps acroasca, Ophiocordyceps bifertilis, Ophiocordyceps subtiliphialida, Ophiocordyceps basiasca, Ophiocordyceps nuozhaduensis and Ophiocordyceps contiispora. Descriptions and illustrations for six taxon were provided. Five of these species were collected from the subtropical monsoon evergreen broad-leaf forest, and one was collected from the rainforest and subtropical monsoon evergreen broad-leaf forest. This work proposes that the same host of Camponotus can be infected by multiple ant pathogenic fungi, while multiple ants of Polyrhachis can be infected by the same pathogenic fungi at the same time. This study contributes towards a better understanding of the evolutionary relationship between hosts and fungi, and provides novel insights into the morphology, distribution, parasitism, and ecology of Ophiocordyceps unilateralis sensu lato. We have provided a method for obtaining living cultures of Ophiocordyceps unilateralis complex species and their asexual morphs based on the living cultures, which is of significant value for further studies of Ophiocordyceps unilateralis complex species in the future.
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Affiliation(s)
- Dexiang Tang
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650504, China
- School of Life Science, Yunnan University, Kunming, 650504, China
| | - Ou Huang
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650504, China
- School of Life Science, Yunnan University, Kunming, 650504, China
| | - Weiqiu Zou
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650504, China
- School of Life Science, Yunnan University, Kunming, 650504, China
| | - Yuanbing Wang
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650504, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yao Wang
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650504, China
| | - Quanying Dong
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650504, China
- School of Life Science, Yunnan University, Kunming, 650504, China
| | - Tao Sun
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650504, China
- School of Life Science, Yunnan University, Kunming, 650504, China
| | - Gang Yang
- The Council of Management and Conservation of Sun River National Park, Puer, 665000, China
| | - Hong Yu
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650504, China.
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20
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Debeljak P, Baltar F. Fungal Diversity and Community Composition across Ecosystems. J Fungi (Basel) 2023; 9:jof9050510. [PMID: 37233221 DOI: 10.3390/jof9050510] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/13/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023] Open
Abstract
Fungi have shaped the biosphere since the development of life on Earth. Despite fungi being present in all environments, most of the available fungal research has focused on soils. As a result, the role and composition of fungal communities in aquatic (marine and freshwater) environments remain largely unexplored. The use of different primers to characterise fungal communities has additionally complicated intercomparisons among studies. Consequently, we lack a basic global assessment of fungal diversity across major ecosystems. Here, we took advantage of a recently published 18S rRNA dataset comprising samples from major ecosystems (terrestrial, freshwater, and marine) to attempt a global assessment of fungal diversity and community composition. We found the highest fungal diversities for terrestrial > freshwater > marine environments, and pronounced gradients of fungal diversity along temperature, salinity, and latitude in all ecosystems. We also identified the most abundant taxa in each of these ecosystems, mostly dominated by Ascomycota and Basidiomycota, except in freshwater rivers where Chytridiomycota dominated. Collectively, our analysis provides a global analysis of fungal diversity across all major environmental ecosystems, highlighting the most distinct order and ASVs (amplicon sequencing variants) by ecosystem, and thus filling a critical gap in the study of the Earth's mycobiome.
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Affiliation(s)
- Pavla Debeljak
- Fungal & Biogeochemical Oceanography, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
- SupBiotech, 94800 Villejuif, France
| | - Federico Baltar
- Fungal & Biogeochemical Oceanography, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
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21
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Aladhadh M. A Review of Modern Methods for the Detection of Foodborne Pathogens. Microorganisms 2023; 11:1111. [PMID: 37317085 DOI: 10.3390/microorganisms11051111] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 06/16/2023] Open
Abstract
Despite the recent advances in food preservation techniques and food safety, significant disease outbreaks linked to foodborne pathogens such as bacteria, fungi, and viruses still occur worldwide indicating that these pathogens still constitute significant risks to public health. Although extensive reviews of methods for foodborne pathogens detection exist, most are skewed towards bacteria despite the increasing relevance of other pathogens such as viruses. Therefore, this review of foodborne pathogen detection methods is holistic, focusing on pathogenic bacteria, fungi, and viruses. This review has shown that culture-based methods allied with new approaches are beneficial for the detection of foodborne pathogens. The current application of immunoassay methods, especially for bacterial and fungal toxins detection in foods, are reviewed. The use and benefits of nucleic acid-based PCR methods and next-generation sequencing-based methods for bacterial, fungal, and viral pathogens' detection and their toxins in foods are also reviewed. This review has, therefore, shown that different modern methods exist for the detection of current and emerging foodborne bacterial, fungal, and viral pathogens. It provides further evidence that the full utilization of these tools can lead to early detection and control of foodborne diseases, enhancing public health and reducing the frequency of disease outbreaks.
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Affiliation(s)
- Mohammed Aladhadh
- Department of Food Science and Human Nutrition, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 51452, Saudi Arabia
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22
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Kelly JR, Clarke G, Harkin A, Corr SC, Galvin S, Pradeep V, Cryan JF, O'Keane V, Dinan TG. Seeking the Psilocybiome: Psychedelics meet the microbiota-gut-brain axis. Int J Clin Health Psychol 2023; 23:100349. [PMID: 36605409 PMCID: PMC9791138 DOI: 10.1016/j.ijchp.2022.100349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/16/2022] [Indexed: 12/15/2022] Open
Abstract
Moving towards a systems psychiatry paradigm embraces the inherent complex interactions across all levels from micro to macro and necessitates an integrated approach to treatment. Cortical 5-HT2A receptors are key primary targets for the effects of serotonergic psychedelics. However, the therapeutic mechanisms underlying psychedelic therapy are complex and traverse molecular, cellular, and network levels, under the influence of biofeedback signals from the periphery and the environment. At the interface between the individual and the environment, the gut microbiome, via the gut-brain axis, plays an important role in the unconscious parallel processing systems regulating host neurophysiology. While psychedelic and microbial signalling systems operate over different timescales, the microbiota-gut-brain (MGB) axis, as a convergence hub between multiple biofeedback systems may play a role in the preparatory phase, the acute administration phase, and the integration phase of psychedelic therapy. In keeping with an interconnected systems-based approach, this review will discuss the gut microbiome and mycobiome and pathways of the MGB axis, and then explore the potential interaction between psychedelic therapy and the MGB axis and how this might influence mechanism of action and treatment response. Finally, we will discuss the possible implications for a precision medicine-based psychedelic therapy paradigm.
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Affiliation(s)
- John R. Kelly
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Sinead C. Corr
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Microbiology, Trinity College Dublin, Ireland
| | - Stephen Galvin
- Department of Psychiatry, Trinity College, Dublin, Ireland
| | - Vishnu Pradeep
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
| | - John F. Cryan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Veronica O'Keane
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
- Trinity College Institute of Neuroscience, Ireland
| | - Timothy G. Dinan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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23
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Bamisile BS, Siddiqui JA, Nie L, Idrees A, Aguila LCR, Jia C, Xu Y. Baseline Analysis of Endophytic Fungal Associates of Solenopsis invicta Buren from Mounds across Five Counties of Guangdong Province, China. J Fungi (Basel) 2023; 9:jof9030377. [PMID: 36983545 PMCID: PMC10058942 DOI: 10.3390/jof9030377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Red imported fire ants mounds have been suggested as a potential reservoir for beneficial entomopathogenic fungal species that are vital for more complex roles in the ecosystem aside from infecting the insects. In the current study, the assemblage of fungal symbionts of the red imported fire ants (RIFA) were obtained across five cities in Guangdong Province, China. The sampling areas were selected because of high occurrence of fire ants mounds in the regions. Mound soils, plant debris within mounds, and ants were collected from three sampling locations in each city for potential isolation of entomopathogenic fungal associates of RIFA. All samples were collected during the spring of 2021. Following successful isolation from substrates, the patterns of fungal species composition, and richness were evaluated. In total, 843 isolates were recovered, and based on their phenotypic distinctiveness and molecular characterization based on DNA sequences of multiple loci including the ITS, SSU, and LSU regions, 46 fungal taxa were obtained, including 12 that were unidentified. Species richness and abundance was highest in the mound soils, while the lowest value was recorded from the ant body. As per the different locations, the highest abundance level was recorded in Zhuhai, where 15 fungal taxa were cultivated. The most common taxa across all substrates and locations was Talaromyces diversus. A baseline analysis of the fungal community composition of RIFA would better our understanding on the interactions between these social ants and their associated microbial organisms, and this knowledge in turn would be important for the successful management of the RIFA.
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Affiliation(s)
- Bamisope Steve Bamisile
- Department of Entomology, South China Agricultural University, Guangzhou 510642, China
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Junaid Ali Siddiqui
- College of Agriculture, College of Tobacco Science, Guizhou University, Guiyang 550025, China
| | - Lei Nie
- Department of Entomology, South China Agricultural University, Guangzhou 510642, China
| | - Atif Idrees
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture, Institute of Entomology, Guizhou University, Guiyang 550025, China
| | - Luis Carlos Ramos Aguila
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Chunsheng Jia
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Yijuan Xu
- Department of Entomology, South China Agricultural University, Guangzhou 510642, China
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24
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Historical biogeography and diversification of ringless Amanita (section Vaginatae) support an African origin and suggest niche conservatism in the Americas. Mol Phylogenet Evol 2023; 178:107644. [PMID: 36243328 DOI: 10.1016/j.ympev.2022.107644] [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: 07/08/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Ectomycorrhizal fungi (ECM) sustain nutrient recycling in most terrestrial ecosystems, yet we know little about what major biogeographical events gave rise to present-day diversity and distribution patterns. Given the strict relationship between some ECM lineages and their hosts, geographically well-sampled phylogenies are central to understanding major evolutionary processes of fungal biodiversity patterns. Here, we focus on Amanita sect. Vaginatae to address global diversity and distribution patterns. Ancestral-state-reconstruction based on a 4-gene timetree with over 200 species supports an African origin between the late Paleocene and the early Eocene (ca. 56 Ma). Major biogeographic "out-of-Africa" events include multiple dispersal events to Southeast Asia (ca. 45-21 Ma), Madagascar (ca. 18 Ma), and the current Amazonian basin (ca. 45-36 Ma), the last two likely trans-oceanic. Later events originating in Southeast Asia involve Nearctic dispersal to North America (ca. 20-5 Ma), Oceania (Australia and New Zealand; ca. 15 Ma), and Europe (ca. 10-5 Ma). Subsequent dispersals were also inferred from Southeast Asia to East Asia (ca. 4 Ma); from North America to East Asia (ca. 11-8 Ma), Southeast Asia (ca. 19-2 Ma), Northern Andes (ca. 15 Ma), and Europe (ca. 15-2 Ma), respectively; and from the Amazon to the Caribbean region (ca. 25-20 Ma). Finally, we detected a significant increase in the net diversification rates in the branch leading to most northern temperate species in addition to higher state-dependent diversification rates in temperate lineages, consistent with previous findings. These results suggest that species of sect. Vaginatae likely have higher dispersal ability and higher adaptability to new environments, in particular compared to those of its sister clade, sect. Caesareae. Overall, the much wider distribution of A. sect. Vaginatae, from pan-tropical to pan-arctic, provides a unique window to understanding niche conservatism across a species-rich clade of ECM fungi.
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25
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Zhang J, Feng N, Liu Y, Zhang H, Yang Y, Liu L, Feng J. Bioactive Compounds from Medicinal Mushrooms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 184:219-268. [PMID: 36244999 DOI: 10.1007/10_2022_202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Research progress of active compounds and biological activities of medicinal mushroom-Ganoderma spp., Hericium spp., Phellinus spp., and Cordyceps spp. were summarized systematically. The main active compounds of medicinal mushrooms included are polysaccharides, proteins, triterpenes, meroterpenoids, polyphenols and nitrogen-containing compounds. The biological activities of the compounds cover immunomodulatory activity, antitumor activity, hypoglycemic activity, hepatoprotective activity, and activity of regulation of intellectual flora.
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Affiliation(s)
- Jingsong Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China.
| | - Na Feng
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Yangfang Liu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Henan Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Yan Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Liping Liu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Jie Feng
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
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26
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Ohmaki A, Okane I, Crous P, Verkley G. Cylindromonium dirinariae sp. nov. ( Ascomycota, Hypocreales), a new nectrioid lichenicolous species on Dirinaria applanata in Japan. Fungal Syst Evol 2023; 11:1-10. [PMID: 37469937 PMCID: PMC10353293 DOI: 10.3114/fuse.2023.11.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/02/2023] [Indexed: 07/21/2023] Open
Abstract
A nectrioid fungus forming a pinkish colony with mainly solitary phialides producing ellipsoid, aseptate conidia in mucoid packets was isolated from Dirinaria applanata. Our taxonomic study based on morphology and phylogenetic analysis using ITS rDNA sequences revealed that the isolates represented a member of the genus Cylindromonium. Based on further morphological examination, nucleotide sequence comparison, and phylogenetic analysis based on LSU rDNA, tef1, and rpb2 in addition to the phylogenetic analysis using the ITS rDNA sequences, the fungus from Dirinaria represents a new species, which is described here as Cylindromonium dirinariae sp. nov. Furthermore, inoculation experiments revealed that this species can also produce perithecia when inoculated on the host lichen in laboratory environments. Citation: Ohmaki A, Okane I, Crous PW, Verkley GJM (2023). Cylindromonium dirinariae sp. nov. (Ascomycota, Hypocreales), a new nectrioid lichenicolous species on Dirinaria applanata in Japan. Fungal Systematics and Evolution 11: 1-10. doi: 10.3114/fuse.2023.11.01.
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Affiliation(s)
- A. Ohmaki
- Agro-Bioresources Science and Technology,
Univ. of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - I. Okane
- Faculty of Life and Environmental Sciences,
Univ. of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute,
Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - G.J.M. Verkley
- Westerdijk Fungal Biodiversity Institute,
Uppsalalaan 8, 3584 CT Utrecht, Netherlands
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27
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Nasif SO, Siddique AB, Siddique AB, Islam MM, Hassan O, Deepo DM, Hossain A. Prospects of endophytic fungi as a natural resource for the sustainability of crop production in the modern era of changing climate. Symbiosis 2022. [DOI: 10.1007/s13199-022-00879-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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28
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Zhang Z, Chen W, Liang J, Zhang L, Han Y, Huang J, Liang Z. Revealing the non-overlapping characteristics between original centers and genetic diversity of Purpureocillium lilacinum. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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29
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Tennakoon DS, Thambugala KM, de Silva NI, Suwannarach N, Lumyong S. A taxonomic assessment of novel and remarkable fungal species in Didymosphaeriaceae ( Pleosporales, Dothideomycetes) from plant litter. Front Microbiol 2022; 13:1016285. [PMID: 36483195 PMCID: PMC9722976 DOI: 10.3389/fmicb.2022.1016285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/11/2022] [Indexed: 05/30/2024] Open
Abstract
Fungal taxonomy has a long history and changed significantly in the last few decades. Most recent studies have witnessed morphology combined with DNA-based molecular analyses as the main research tool for fungal species identification. During field surveys, some interesting Didymosphaeriaceae species were found from plant litter in China and Thailand. Morphology combined with phylogenetic analyses (Bayesian and maximum likelihood) of ITS, LSU, SSU, tef1-α, and tub2 loci was used to identify fungal taxa. In this article, three new species and six new host records are described. The new species, Montagnula acaciae, Paraconiothyrium zingiberacearum, and Paraphaeosphaeria brachiariae, can be distinguished from other species of the respective genera based on their distinct size differences (ascomata, asci, and ascospores) and DNA sequence data. The new host records, Montagnula jonesii, Paraconiothyrium fuckelii, Spegazzinia deightonii, and S. tessarthra are reported from Ficus benjamina, Dimocarpus longan, Hedychium coronarium, and Acacia auriculiformis respectively, for the first time. Also, Paraconiothyrium archidendri and P. brasiliense are reported for the first time from Magnolia sp. in China. Moreover, Paraconiothyrium rosae is synonymized under P. fuckelii based on close phylogeny affinities and morphological characteristics. In-depth morphological descriptions, micrographs, and phylogenetic trees are provided to show the placement of new taxa.
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Affiliation(s)
- Danushka S. Tennakoon
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Kasun M. Thambugala
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Sri Lanka
| | - Nimali I. de Silva
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Saisamorn Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
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30
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Pereira Dos Santos VH, Luiz JHH, Dos Anjos JP, de Oliveira Silva E. Oxidative potential of two Brazilian endophytic fungi from Handroanthus impetiginosus towards progesterone. Steroids 2022; 187:109101. [PMID: 35970224 DOI: 10.1016/j.steroids.2022.109101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/26/2022]
Abstract
Biotransformation has been successfully employed to conduct uncommon reactions, which would hardly be carried out by chemical synthesis. A wide diversity of compounds may be metabolized by fungi, leading to chemical derivatives through selective reactions that work under ecofriendly conditions. Endophytic fungi live inside vegetal tissues without causing damage to the host plant, making available unique enzymes for interesting chemical derivatization. Biotransformation of steroids by endophytic fungi may provide new derivatives as these microorganisms came from uncommon and underexplored habitats. In this study, endophytic strains isolated from Handroanthus impetiginosus leaves were assayed for biotransformation of progesterone, and its derivatives were identified through GC-EI-MS analysis. The endophyte Talaromyces sp. H4 was capable of transforming the steroidal nucleus selectively into four products through selective ene-reduction of the C4-C5 double bond and C-17 oxidation. The best conversion rate of progesterone (>90 %) was reached with Penicillium citrinum H7 endophytic strain that transformed the substrate into one derivative. The results highlight endophytic fungi's potential to obtain new and interesting steroidal derivatizations.
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Affiliation(s)
| | | | - Jeancarlo Pereira Dos Anjos
- University Center SENAI CIMATEC, Salvador, BA, Brazil; INCT in Energy and Environment, Federal University of Bahia, Salvador, BA, Brazil
| | - Eliane de Oliveira Silva
- Departament of Organic Chemistry, Chemistry Institute, Federal University of Bahia, Salvador, BA, Brazil.
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31
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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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Bartoszewicz JM, Nasri F, Nowicka M, Renard BY. Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection. Bioinformatics 2022; 38:ii168-ii174. [PMID: 36124807 DOI: 10.1093/bioinformatics/btac495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Emerging pathogens are a growing threat, but large data collections and approaches for predicting the risk associated with novel agents are limited to bacteria and viruses. Pathogenic fungi, which also pose a constant threat to public health, remain understudied. Relevant data remain comparatively scarce and scattered among many different sources, hindering the development of sequencing-based detection workflows for novel fungal pathogens. No prediction method working for agents across all three groups is available, even though the cause of an infection is often difficult to identify from symptoms alone. RESULTS We present a curated collection of fungal host range data, comprising records on human, animal and plant pathogens, as well as other plant-associated fungi, linked to publicly available genomes. We show that it can be used to predict the pathogenic potential of novel fungal species directly from DNA sequences with either sequence homology or deep learning. We develop learned, numerical representations of the collected genomes and visualize the landscape of fungal pathogenicity. Finally, we train multi-class models predicting if next-generation sequencing reads originate from novel fungal, bacterial or viral threats. CONCLUSIONS The neural networks trained using our data collection enable accurate detection of novel fungal pathogens. A curated set of over 1400 genomes with host and pathogenicity metadata supports training of machine-learning models and sequence comparison, not limited to the pathogen detection task. AVAILABILITY AND IMPLEMENTATION The data, models and code are hosted at https://zenodo.org/record/5846345, https://zenodo.org/record/5711877 and https://gitlab.com/dacs-hpi/deepac. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jakub M Bartoszewicz
- Hasso Plattner Institute for Digital Engineering, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany.,Department of Mathematics and Computer Science, Free University of Berlin, Berlin 14195, Germany
| | - Ferdous Nasri
- Hasso Plattner Institute for Digital Engineering, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany.,Department of Mathematics and Computer Science, Free University of Berlin, Berlin 14195, Germany
| | - Melania Nowicka
- Hasso Plattner Institute for Digital Engineering, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany.,Department of Mathematics and Computer Science, Free University of Berlin, Berlin 14195, Germany
| | - Bernhard Y Renard
- Hasso Plattner Institute for Digital Engineering, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
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Su W, Xu R, Bhunjun CS, Tian S, Dai Y, Li Y, Phukhamsakda C. Diversity of Ascomycota in Jilin: Introducing Novel Woody Litter Taxa in Cucurbitariaceae. J Fungi (Basel) 2022; 8:jof8090905. [PMID: 36135630 PMCID: PMC9501381 DOI: 10.3390/jof8090905] [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: 07/15/2022] [Revised: 08/12/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
Cucurbitariaceae has a high biodiversity worldwide on various hosts and is distributed in tropical and temperate regions. Woody litters collected in Changchun, Jilin Province, China, revealed a distinct collection of fungi in the family Cucurbitariaceae based on morphological and molecular data. Phylogenetic analyses of the concatenated matrix of the internal transcribed spacer (ITS) region, the large subunit (LSU) of ribosomal DNA, the RNA polymerase II subunit (rpb2), the translation elongation factor 1-alpha (tef1-α) and β-tubulin (β-tub) genes indicated that the isolates represent Allocucurbitaria and Parafenestella species based on maximum likelihood (ML), maximum parsimony (MP) and Bayesian analysis (BPP). We report four novel species: Allocucurbitaria mori, Parafenestella changchunensis, P. ulmi and P. ulmicola. The importance of five DNA markers for species-level identification in Cucurbitariaceae was determined by Assemble Species by Automatic Partitioning (ASAP) analyses. The protein-coding gene β-tub is determined to be the best marker for species level identification in Cucurbitariaceae.
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Affiliation(s)
- Wenxin Su
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Rong Xu
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Chitrabhanu S. Bhunjun
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Shangqing Tian
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Yueting Dai
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Yu Li
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (Y.L.); (C.P.)
| | - Chayanard Phukhamsakda
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (Y.L.); (C.P.)
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Byregowda R, Prasad SR, Oelmüller R, Nataraja KN, Prasanna Kumar MK. Is Endophytic Colonization of Host Plants a Method of Alleviating Drought Stress? Conceptualizing the Hidden World of Endophytes. Int J Mol Sci 2022; 23:ijms23169194. [PMID: 36012460 PMCID: PMC9408852 DOI: 10.3390/ijms23169194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
In the wake of changing climatic conditions, plants are frequently exposed to a wide range of biotic and abiotic stresses at various stages of their development, all of which negatively affect their growth, development, and productivity. Drought is one of the most devastating abiotic stresses for most cultivated crops, particularly in arid and semiarid environments. Conventional breeding and biotechnological approaches are used to generate drought-tolerant crop plants. However, these techniques are costly and time-consuming. Plant-colonizing microbes, notably, endophytic fungi, have received increasing attention in recent years since they can boost plant growth and yield and can strengthen plant responses to abiotic stress. In this review, we describe these microorganisms and their relationship with host plants, summarize the current knowledge on how they “reprogram” the plants to promote their growth, productivity, and drought tolerance, and explain why they are promising agents in modern agriculture.
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Affiliation(s)
- Roopashree Byregowda
- Department of Seed Science and Technology, University of Agricultural Sciences, Bangalore 560065, India
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University, 07743 Jena, Germany
| | | | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University, 07743 Jena, Germany
- Correspondence:
| | - Karaba N. Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore 560065, India
| | - M. K. Prasanna Kumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore 560065, India
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35
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Fungal community succession on decomposing leaf litter across five phylogenetically related tree species in a subtropical forest. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00508-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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36
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Strassert JFH, Monaghan MT. Phylogenomic insights into the early diversification of fungi. Curr Biol 2022; 32:3628-3635.e3. [PMID: 35830854 DOI: 10.1016/j.cub.2022.06.057] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/10/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022]
Abstract
Phylogenomic analyses have boosted our understanding of the evolutionary trajectories of all living forms by providing continuous improvements to the tree of life.1-5 Within this tree, fungi represent an ancient eukaryote group,6 having diverged from the animals ∼1.35 billion years ago.7 Estimates of the number of extant species range between 1.5 and 3.8 million.8,9 Recent reclassifications and the discovery of the deep-branching Sanchytriomycota lineage10 have brought the number of proposed phyla to 20,11 21 if the Microsporidia are included.12-14 Uncovering how the diverse and globally distributed fungi are related to each other is fundamental for understanding how their lifestyles, morphologies, and metabolic capacities evolved. To date, many of the proposed relationships among the phyla remain controversial and no phylogenomic study has examined the entire fungal tree using a taxonomically comprehensive dataset and suitable models of evolution. We assembled and curated a 299-protein dataset with a taxon sampling broad enough to encompass all recognized fungal diversity with available data, but selective enough to run computationally intensive analyses using best-fitting models. Using a range of reconstruction methods, we were able to resolve many contested nodes, such as a sister relationship of Chytridiomyceta to all other non-Opisthosporidia fungi (with Chytridiomycota being sister to Monoblepharomycota + Neocallimastigomycota), a branching of Blastocladiomycota + Sanchytriomycota after the Chytridiomyceta but before other non-Opisthosporidia fungi, and a branching of Glomeromycota as sister to the Dikarya. Our up-to-date fungal tree of life will serve as a springboard for future investigations on the early evolution of fungi.
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Affiliation(s)
- Jürgen F H Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.
| | - Michael T Monaghan
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
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Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. mSystems 2022; 7:e0023222. [PMID: 35638725 PMCID: PMC9239088 DOI: 10.1128/msystems.00232-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Secondary metabolite clusters (SMCs) encode the machinery for fungal toxin production. However, understanding their function and analyzing their products requires investigation of the developmental and environmental conditions in which they are expressed. Gene expression is often restricted to specific and unexamined stages of the life cycle. Therefore, we applied comparative genomics analyses to identify SMCs in Neurospora crassa and analyzed extensive transcriptomic data spanning nine independent experiments from diverse developmental and environmental conditions to reveal their life cycle-specific gene expression patterns. We reported 20 SMCs comprising 177 genes-a manageable set for investigation of the roles of SMCs across the life cycle of the fungal model N. crassa-as well as gene sets coordinately expressed in 18 predicted SMCs during asexual and sexual growth under three nutritional and two temperature conditions. Divergent activity of SMCs between asexual and sexual development was reported. Of 126 SMC genes that we examined for knockout phenotypes, al-2 and al-3 exhibited phenotypes in asexual growth and conidiation, whereas os-5, poi-2, and pmd-1 exhibited phenotypes in sexual development. SMCs with annotated function in mating and crossing were actively regulated during the switch between asexual and sexual growth. Our discoveries call for attention to roles that SMCs may play in the regulatory switches controlling mode of development, as well as the ecological associations of those developmental stages that may influence expression of SMCs. IMPORTANCE Secondary metabolites (SMs) are low-molecular-weight compounds that often mediate interactions between fungi and their environments. Fungi enriched with SMs are of significant research interest to agriculture and medicine, especially from the aspects of pathogen ecology and environmental epidemiology. However, SM clusters (SMCs) that have been predicted by comparative genomics alone have typically been poorly defined and insufficiently functionally annotated. Therefore, we have investigated coordinate expression in SMCs in the model system N. crassa, and our results suggest that SMCs respond to environmental signals and to stress that are associated with development. This study examined SMC regulation at the level of RNA to integrate observations and knowledge of these genes in various growth and development conditions, supporting combining comparative genomics and inclusive transcriptomics to improve computational annotation of SMCs. Our findings call for detailed study of the function of SMCs during the asexual-sexual switch, a key, often-overlooked developmental stage.
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Aguiar LO, Silva EDO, David JM. Biotransformation of chalcones and flavanones: An update on their bio-based derivatizations. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2073226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
| | | | - Jorge M. David
- Instituto de Química, Universidade Federal da Bahia, Salvador, Brazil
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39
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Permana D, Niesel K, Ford MJ, Ichinose H. Latent Functions and Applications of Cytochrome P450 Monooxygenases from Thamnidium elegans: A Novel Biocatalyst for 14α-Hydroxylation of Testosterone. ACS OMEGA 2022; 7:13932-13941. [PMID: 35559141 PMCID: PMC9088945 DOI: 10.1021/acsomega.2c00430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/05/2022] [Indexed: 05/21/2023]
Abstract
Cytochrome P450 monooxygenases (P450s) are ubiquitous enzymes with high availability and diversity in nature. Fungi provide a diverse and complex array of P450s, and these enzymes play essential roles in various secondary metabolic processes. Besides the physiological impacts of P450s on fungal life, their versatile functions are attractive for use in advanced applications of the biotechnology sector. Herein, we report gene identification and functional characterization of P450s from the zygomycetous fungus Thamnidium elegans (TeCYPs). We identified 48 TeCYP genes, including two putative pseudogenes, from the whole-genome sequence of T. elegans. Furthermore, we constructed a functional library of TeCYPs and heterologously expressed 46 TeCYPs in Saccharomyces cerevisiae. Recombinants of S. cerevisiae were then used as whole-cell biocatalysts for bioconversion of various compounds. Catalytic potentials of various TeCYPs were demonstrated through a functionomic survey to convert a series of compounds, including steroidal substrates. Notably, CYP5312A4 was found to be highly active against testosterone. Based on nuclear magnetic resonance analysis, enzymatic conversion of testosterone to 14α-hydroxytestosterone by CYP5312A4 was demonstrated. This is the first report to identify a novel fungal P450 that catalyzes the 14α-hydroxylation of testosterone. In addition, we explored the latent potentials of TeCYPs using various substrates. This study provides a platform to further study the potential use of TeCYPs as catalysts in pharmaceutical and agricultural industries and biotechnology.
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Affiliation(s)
- Dani Permana
- Faculty
of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Research
Center for Environmental and Clean Technology, The National Research and Innovation Agency of the Republic of Indonesia
(BRIN), Bandung Advanced Science and Creative Engineering Space (BASICS), Jl. Cisitu, Bandung 40135, Indonesia
| | - Ksenia Niesel
- Bayer
AG, Industriepark Höchst, Frankfurt am Main 65926, Germany
| | | | - Hirofumi Ichinose
- Faculty
of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- . Phone/Fax: +81 (0)92-802-4666
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Magnago AC, Alves-Silva G, Henkel TW, da Silveira RMB. New genera, species, and combinations of Boletaceae from Brazil and Guyana. Mycologia 2022; 114:1-19. [PMID: 35452350 DOI: 10.1080/00275514.2022.2037307] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/31/2022] [Indexed: 10/18/2022]
Abstract
Brasilioporus olivaceoflavidus, gen. et sp. nov., Brasilioporus simoniarum, sp. nov., Neotropicomus australis, gen. et sp. nov., and Nevesoporus nigrostipitatus, gen. et sp. nov. (Boletaceae, Boletales, Basidiomycota), are described from the endangered Atlantic Forest biome of eastern Brazil. New combinations into these new genera are proposed for the Guyanese taxa Xerocomus parvogracilis, Tylopilus rufonigricans, and Tylopilus exiguus. Boletaceae subfamily Chalciporoideae was recircumscribed to include the new genus Nevesoporus. Molecular phylogenetic analyses using a multilocus data set (ITS+28S+TEF1+RPB1+RPB2) from a large taxon set across the Boletaceae justify recognition of the new genera. Morphological, ecological, and DNA sequence data are provided for the new species. A key to known native and introduced bolete species from the Brazilian Atlantic Forest is provided.
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Affiliation(s)
- Altielys Casale Magnago
- Departamento de Botânica, Universidade Federal do Espírito Santo, Campus Goiabeiras, Vitória, 29075-910, Brazil
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, 91509-900, Brazil
| | - Genivaldo Alves-Silva
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, 91509-900, Brazil
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi), Universidade Federal de Santa Catarina, Florianópolis, 88040-900, Brazil
- Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Campus Reitor João David Ferreira Lima, Florianópolis, 88040-900, Brazil
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, California 95521, USA
| | - Rosa Mara Borges da Silveira
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, 91509-900, Brazil
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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: 3] [Impact Index Per Article: 1.5] [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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Wanasinghe DN, Ren GC, Xu JC, Cheewangkoon R, Mortimer PE. Insight into the Taxonomic Resolution of the Pleosporalean Species Associated with Dead Woody Litter in Natural Forests from Yunnan, China. J Fungi (Basel) 2022; 8:jof8040375. [PMID: 35448606 PMCID: PMC9033009 DOI: 10.3390/jof8040375] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 01/19/2023] Open
Abstract
In the course of investigating the systematics of woody litter micromycete associates in Yunnan Province, China, we found one new species in Phaeoseptaceae, one new genus and three new species in Sulcatisporaceae from 16 specimens collected (ten collections of ascomycetous teleomorphs, four collections of hyphomycetous and two collections of coelomycetes anamorphs) from Ailaoshan, Chuxiong, Diqing, Honghe, Kunming, Lancang, Mengla and Yuxi in Yunnan Province. These taxonomic novelties were recognized with the aid of morphological comparisons and phylogenetic analyses of multiple gene sequences (non-translated loci and protein-coding regions). Pleopunctum menglaense sp. nov. is accommodated in Phaeoseptaceae (Pleosporales) based on its hyphomycetous anamorph, which is characterized by superficial sporodochia on the host surface, macronematous, mononematous, cylindrical, unbranched, aseptate, hyaline and smooth-walled conidiophores, monoblastic, terminal, hyaline conidiogenous cells, hyaline, muriform α conidia, and brown, muriform β conidia with tri-lobed wing like basal cells. Kazuakitanaka gen. nov. (type: K. yuxiensis) is introduced in Sulcatisporaceae (Massarineae, Pleosporales) for a saprobic ascomycete with teleomorphic and anamorphic (coelomycetous) features. The teleomorph possesses globose to subglobose ascomata with acentric ostiole, a peridial wall of textura angularis to textura prismatica, cylindric-clavate, pedicellate asci with an ocular chamber, and 1–2-septate, hyaline, fusiform, guttulate ascospores with a distinct mucilaginous sheath. The anamorph features pycnidial conidiomata, phialidic, ampulliform to cylindrical, hyaline conidiogenous cells and ampulliform to cylindrical, one-to-three-septate, hyaline, guttulate conidia. Loculosulcatispora was known only from its anamorph of L. thailandica. We observed the teleomorph of Loculosulcatispora hongheensis sp. nov. and amended the generic description of Loculosulcatispora accordingly. Loculosulcatispora hongheensis is characterized by globose to subglobose ascomata with a central ostiole, a peridial wall of textura angularis to globosa, branched, septate, pseudoparaphyses, clavate asci with a short pedicel and a minute ocular chamber and hyaline, fusiform, 1-septate ascospores with a thick irregular mucilaginous sheath. This study provides some insights into the diversity of fungi on dead woody litter in terrestrial habitats.
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Affiliation(s)
- Dhanushka N. Wanasinghe
- Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe 654400, China; (D.N.W.); (J.-C.X.)
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Guang-Cong Ren
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand;
| | - Jian-Chu Xu
- Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe 654400, China; (D.N.W.); (J.-C.X.)
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CIFOR-ICRAF China Program, World Agroforestry (ICRAF), Kunming 650201, China
| | - Ratchadawan Cheewangkoon
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (R.C.); (P.E.M.)
| | - Peter E. Mortimer
- Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe 654400, China; (D.N.W.); (J.-C.X.)
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Correspondence: (R.C.); (P.E.M.)
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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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Forecasting the number of species of asexually reproducing fungi (Ascomycota and Basidiomycota). FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00500-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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New Records of Powdery Mildews from Taiwan: Erysiphe ipomoeae comb. nov., E. aff. betae on Buckwheat, and E. neolycopersici comb. nov. on Cardiospermum halicacabum. DIVERSITY 2022. [DOI: 10.3390/d14030204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Erysiphe is the largest genus of powdery mildews (PMs), a group of obligate plant pathogenic fungi. Exploration of biodiversity generally relies on regional surveys and our aim is to investigate the PMs in Taiwan. Collections of the fungi on five plant species around agricultural environments were subjected to morphological and molecular characterization, using both internal transcribed spacer (ITS) and β-tubulin gene (TUB2) regions for the phylogenetic analyses. Erysipheipomoeae comb. nov., a species able to infect Ipomoea obscura and I. aquatica demonstrated by pathogenicity tests, has been neotypified. The two buckwheat species, Fagopyrum esculentum and F. tataricum, are found to be hosts of E. aff. betae. These results suggest that hosts in some plant families can be infected by more than one Erysiphe pathogen, e.g., Convolvulaceae by E. ipomoeae and E. convolvuli and Polygonaceae by E. polygoni and E. aff. betae, respectively. In addition, phylogenetic analyses of PMs on Cardiospermum halicacabum and tomato belonging to the E. aquilegiae complex are allocated under E. neolycopersici comb. nov. This extends the potential host range of E. aquilegiae complex to the plant family Sapindaceae. We conclude that awareness of the host associations of PMs can potentially benefit crop disease management.
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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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Bruun HH, Brunbjerg AK, Dalby L, Fløjgaard C, Frøslev TG, Haarder S, Heilmann‐Clausen J, Høye TT, Læssøe T, Ejrnæs R. Simple attributes predict the value of plants as hosts to fungal and arthropod communities. OIKOS 2022. [DOI: 10.1111/oik.08823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Lars Dalby
- Dept of Ecoscience, Aarhus Univ. Rønde Denmark
| | | | | | | | | | | | - Thomas Læssøe
- Dept of Biology, Univ. of Copenhagen Copenhagen Denmark
- Centre for Macroecology, Evolution and Climate, Univ. of Copenhagen Copenhagen Denmark
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Al-Kharousi M, Hussain S, Al-Muharabi MA, Al-Shabibi Z, Al-Maqbali D, Al-Balushi AH, Al-Yahya’ei MN, Al-Saady N, Velazhahan R, Al-Sadi AM. The Genus Xanthagaricus: An Updated Global Species Distribution and Phylogeny with the Description of Two New Species from Oman. J Fungi (Basel) 2022; 8:jof8020173. [PMID: 35205927 PMCID: PMC8874380 DOI: 10.3390/jof8020173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 12/10/2022] Open
Abstract
Xanthagaricus is a saprotrophic mushroom genus with small-sized basidiomata in the family Agaricaceae (Agaricales). Prior to this study, 26 species belonging to this genus have been described and published. In this study, we reported Xanthagaricus for the first time from Oman with the description of two new species. Basidiomata of the new species Xanthagaricus appendiculatus and X. omanicus were collected during the monsoon rains of summer in 2018 in the southern coastal region of Oman. Species descriptions are based on morphological and molecular characterization. Phylogenetic analyses based on internal transcribed spacer region (ITS1-5.8S-ITS2 = ITS) of the nuclear ribosomal DNA clustered the new species in the Xanthagaricus clade with strong statistical support. The new species Xanthagaricusappendiculatus can be distinguished from other species by its purplish pileus with umbonate disc and X. omanicus with the largest pileus (70–90 mm diameter) among the known species of the genus. A detailed description, photographs, line drawings, and a phylogenetic tree showing the position of both new species are provided. A dichotomous key to the known taxa of Xanthagaricus is proposed. Morphological comparisons of new species with known Xanthagaricus taxa are provided. Our observations highlight the diversity of Xanthagaricus and other lepiotaceous mushrooms in southern Oman and further document the need for additional systematic focus on the region’s fungi.
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Affiliation(s)
- Moza Al-Kharousi
- Oman Animal and Plant Genetic Resources Center (Mawarid), Ministry of Higher Education, Research and Innovation, P.O. Box 515, Muscat 123, Oman; (M.A.-K.); (Z.A.-S.); (D.A.-M.); (A.H.A.-B.); (M.N.A.-Y.); (N.A.-S.)
| | - Shah Hussain
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34, Al Khoud 123, Oman; (S.H.); (R.V.)
| | - Marwa A. Al-Muharabi
- Sultan Qaboos Comprehensive Cancer Care & Research Center, P.O. Box 566, Al Khoud 123, Oman;
| | - Zahra Al-Shabibi
- Oman Animal and Plant Genetic Resources Center (Mawarid), Ministry of Higher Education, Research and Innovation, P.O. Box 515, Muscat 123, Oman; (M.A.-K.); (Z.A.-S.); (D.A.-M.); (A.H.A.-B.); (M.N.A.-Y.); (N.A.-S.)
| | - Dua’a Al-Maqbali
- Oman Animal and Plant Genetic Resources Center (Mawarid), Ministry of Higher Education, Research and Innovation, P.O. Box 515, Muscat 123, Oman; (M.A.-K.); (Z.A.-S.); (D.A.-M.); (A.H.A.-B.); (M.N.A.-Y.); (N.A.-S.)
| | - Abdullah H. Al-Balushi
- Oman Animal and Plant Genetic Resources Center (Mawarid), Ministry of Higher Education, Research and Innovation, P.O. Box 515, Muscat 123, Oman; (M.A.-K.); (Z.A.-S.); (D.A.-M.); (A.H.A.-B.); (M.N.A.-Y.); (N.A.-S.)
| | - Mohamed N. Al-Yahya’ei
- Oman Animal and Plant Genetic Resources Center (Mawarid), Ministry of Higher Education, Research and Innovation, P.O. Box 515, Muscat 123, Oman; (M.A.-K.); (Z.A.-S.); (D.A.-M.); (A.H.A.-B.); (M.N.A.-Y.); (N.A.-S.)
| | - Nadiya Al-Saady
- Oman Animal and Plant Genetic Resources Center (Mawarid), Ministry of Higher Education, Research and Innovation, P.O. Box 515, Muscat 123, Oman; (M.A.-K.); (Z.A.-S.); (D.A.-M.); (A.H.A.-B.); (M.N.A.-Y.); (N.A.-S.)
| | - Rethinasamy Velazhahan
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34, Al Khoud 123, Oman; (S.H.); (R.V.)
| | - Abdullah M. Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34, Al Khoud 123, Oman; (S.H.); (R.V.)
- Correspondence: ; Tel.: +968-99424633
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Gad M, Hou L, Cao M, Adyari B, Zhang L, Qin D, Yu CP, Sun Q, Hu A. Tracking microeukaryotic footprint in a peri-urban watershed, China through machine-learning approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150401. [PMID: 34562761 DOI: 10.1016/j.scitotenv.2021.150401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/17/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Microeukaryotes play a significant role in biogeochemical cycling and can serve as bioindicators of water quality in freshwater ecosystems. However, there is a knowledge gap on how freshwater microeukaryotic communities are assembled, especially that how terrestrial microeukaryotes influence freshwater microeukaryotic assemblages. Here, we used a combination of 18S rRNA gene amplicon sequencing and community-based microbial source tracking (MST) approaches (i.e., SourceTracker and FEAST) to assess the contribution of microeukaryotes from surrounding environments (i.e., soils, river sediments, swine wastewater, influents and effluents of decentralized wastewater treatment plants) to planktonic microeukaryotes in the main channel, tributaries and reservoir of a peri-urban watershed, China in wet and dry seasons. The results indicated that SAR (~ 49% of the total communities), Opithokonta (~ 34%), Archaeplastida (~ 9%), and Amoebozoa (~ 2%) were dominant taxa in the watershed. The community-based MST analysis revealed that sewage effluents (7.96 - 21.84%), influents (2.23 - 13.97%), and river sediments (2.56 - 11.71%) were the major exogenous sources of riverine microeukaryotes. At the spatial scale, the downstream of the watershed (i.e., main channel and tributaries) received higher proportions of exogenous microeukaryotic OTUs compared to the upstream reservoirs, while at the seasonal scale, the sewage effluents and influents contributed higher exogenous microeukaryotes to river water in wet season than in dry season. Moreover, the swine and domestic wastewater led to the presence of Apicomplexa in wet season only, implying rainfall runoff may enhance the spread of parasitic microeukaryotes. Taken together, our study provides novel insights into the immigration patterns of microeukaryotes and their dominant supergroups between terrestrial and riverine habitats.
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Affiliation(s)
- Mahmoud Gad
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Water Pollution Research Department, National Research Centre, Giza 12622, Egypt
| | - Liyuan Hou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Meixian Cao
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bob Adyari
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Environmental Engineering, Universitas Pertamina, Jakarta 12220, Indonesia
| | - Lanping Zhang
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Qin
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Qian Sun
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Anyi Hu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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