201
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Miguel GA, Carlsen S, Arneborg N, Saerens SM, Laulund S, Knudsen GM. Non-Saccharomyces yeasts for beer production: Insights into safety aspects and considerations. Int J Food Microbiol 2022; 383:109951. [DOI: 10.1016/j.ijfoodmicro.2022.109951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 11/05/2022]
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202
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Chen JH, Shen S, Zhou LW. Modeling current geographic distribution and future range shifts of Sanghuangporus under multiple climate change scenarios in China. Front Microbiol 2022; 13:1064451. [PMID: 36532484 PMCID: PMC9751338 DOI: 10.3389/fmicb.2022.1064451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/09/2022] [Indexed: 09/11/2024] Open
Abstract
The genus Sanghuangporus is well-known for its edible and medicinal values. In this study, the most comprehensive occurrence records of Sanghuangporus with accurate species identification are subjected to MaxEnt, to model the current geographic distribution and future range shifts under multiple climate change scenarios in China. The current potential distribution model of Sanghuangporus is excellently predicted as indicated by the value of Area Under Receiver Operator Characteristic Curve. The current potential distribution basically corresponds to the known occurrence records of Sanghuangporus, and provides clues to new suitable habitats. The critical environmental variables to the distribution are annual precipitation, host plant, annual mean temperature and elevation. Host plant is not the most critical contribution to the model, but it indeed plays a decisive role in restricting the distribution of Sanghuangporus. This role is further confirmed by the distribution area of the highly suitable habitat increasing by 155.468%, when excluding host plant from environmental variables. For future scenarios, generally the area of highly suitable habitat for Sanghuangporus extremely increases, but the locations do not change a lot. In conclusion, this study provides important ecological information for the utilization and conservation of the edible and medicinal fungus Sanghuangporus.
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Affiliation(s)
- Jia-He Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, Liaoning University, Shenyang, China
| | - Shan Shen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, Liaoning University, Shenyang, China
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203
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Yang Y, Lu W, Zhang X, Wu C. Gut fungi differentially response to the antipyretic (heat-clearing) and diaphoretic (exterior-releasing) traditional Chinese medicines in Coptis chinensis-conditioned gut microbiota. Front Pharmacol 2022; 13:1032919. [PMID: 36467054 PMCID: PMC9716107 DOI: 10.3389/fphar.2022.1032919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 03/05/2025] Open
Abstract
Antipyretic (heat-clearing) and diaphoretic (exterior-releasing) drugs are two main groups of traditional Chinese medicines (TCMs) possessing anti-microbes and anti-inflammation effects, with the former mainly through clearing pyrogens while the latter through promoting diaphoresis. Although anti-microorganism is a common action of these two kinds of TCMs, their difference in antimicrobial spectrums and their interactions when combinedly used remain unclear. Herein, we prepared aqueous extracts from Coptis chinensis (HL) and other antipyretic or diaphoretic TCMs, orally administrated them to C57BL/6 mice at a clinical dose for fourteen days, and analyzed their impaction on both gut bacteria and fungi using full-length 16 S rRNA gene sequencing and internal transcribed spacer 1/2 (ITS1/2) gene sequencing, respectively. Oral administration of HL significantly changed the structure of gut bacteria but showed little influence on gut fungi. Co-treatment with antipyretic or diaphoretic TCMs alleviated the impact of HL on gut bacteria to a similar degree. However, combined with either heat-clearing or exterior-releasing TCMs significantly strengthened the influence of HL on gut fungi, with the latter superior to the former. The antipyretic TCMs enriched Penicillium spp. while diaphoretic TCMs promoted Fusarium spp. Further analysis revealed that the diaphoretic TCMs-enriched fungi Fusarium spp. were positively related to Akkermansia spp., a beneficial bacterium that interacts with Toll-like receptor 4 (TLR4) and regulates thermogenesis, thus providing a potential linkage with their pro-diaphoresis effect. Together, our results reveal that gut fungi differentially respond to the impact of heat-clearing and exterior-releasing TCMs on Coptis chinensis-conditioned gut microbiota, which provides insights into their functional characteristics.
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Affiliation(s)
- Yanan Yang
- Pharmacology and Toxicology Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Weiying Lu
- Reproductive Medical Center, Hainan Woman and Children’s Medical Center, Haikou, China
| | - Xiaopo Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical TCMs, School of Pharmacy, Hainan Medical University, Haikou, China
| | - Chongming Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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204
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Kestel JH, Field DL, Bateman PW, White NE, Allentoft ME, Hopkins AJM, Gibberd M, Nevill P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157556. [PMID: 35882340 DOI: 10.1016/j.scitotenv.2022.157556] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia.
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Anna J M Hopkins
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Mark Gibberd
- Centre for Crop Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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205
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Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, Glass NL, Gow NAR, Gurr SJ, Hittinger CT, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE. The future of fungi: threats and opportunities. G3 (BETHESDA, MD.) 2022; 12:jkac224. [PMID: 36179219 PMCID: PMC9635647 DOI: 10.1093/g3journal/jkac224] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/12/2022] [Indexed: 01/13/2023]
Abstract
The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global trade, environmental degradation, and novel viruses altering the impact of fungi on health and disease, developing new approaches is now more crucial than ever to combat the threats posed by fungi and to harness their extraordinary potential for applications in human health, food supply, and environmental remediation. To address this aim, the Canadian Institute for Advanced Research (CIFAR) and the Burroughs Wellcome Fund convened a workshop to unite leading experts on fungal biology from academia and industry to strategize innovative solutions to global challenges and fungal threats. This report provides recommendations to accelerate fungal research and highlights the major research advances and ideas discussed at the meeting pertaining to 5 major topics: (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom, including novel medicines and enzymes.
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Affiliation(s)
- Nicola T Case
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - David S Blehert
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | - Robert A Cramer
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Christina Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Iuliana V Ene
- Department of Mycology, Institut Pasteur, Université de Paris, Paris 75015, France
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London W2 1PG, UK
| | | | - Aleeza C Gerstein
- Department of Microbiology and Department of Statistics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
| | - Neil A R Gow
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sarah J Gurr
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Iliyan D Iliev
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA
| | - Bruce S Klein
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Internal Medicine, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - James W Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jeffrey M Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | | | - Aaron P Mitchell
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Donald C Sheppard
- McGill Interdisciplinary Initiative in Infection and Immunology, Departments of Medicine, Microbiology & Immunology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94117, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA
| | - Eva E Stukenbrock
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Environmental Genomics, Christian-Albrechts University, Kiel 24118, Germany
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California—Berkeley, Berkeley, CA 94720, USA
| | | | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
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206
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Vitte J, Michel M, Malinovschi A, Caminati M, Odebode A, Annesi-Maesano I, Caimmi DP, Cassagne C, Demoly P, Heffler E, Menu E, Nwaru BI, Sereme Y, Ranque S, Raulf M, Feleszko W, Janson C, Galán C. Fungal exposome, human health, and unmet needs: A 2022 update with special focus on allergy. Allergy 2022; 77:3199-3216. [PMID: 35976185 DOI: 10.1111/all.15483] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/01/2022] [Accepted: 08/13/2022] [Indexed: 01/28/2023]
Abstract
Humans inhale, ingest, and touch thousands of fungi each day. The ubiquity and diversity of the fungal kingdom, reflected by its complex taxonomy, are in sharp contrast with our scarce knowledge about its distribution, pathogenic effects, and effective interventions at the environmental and individual levels. Here, we present an overview of salient features of fungi as permanent players of the human exposome and key determinants of human health, through the lens of fungal allergy and other fungal hypersensitivity reactions. Improved understanding of the fungal exposome sheds new light on the epidemiology of fungal-related hypersensitivity diseases, their immunological substratum, the currently available methods, and biomarkers for environmental and medical fungi. Unmet needs are described and potential approaches are highlighted as perspectives.
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Affiliation(s)
- Joana Vitte
- IDESP, University of Montpellier and INSERM, Montpellier, France.,MEPHI, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Moïse Michel
- IDESP, University of Montpellier and INSERM, Montpellier, France.,MEPHI, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France.,Immunology Laboratory, University Hospital Nîmes, Nîmes, France
| | - Andrei Malinovschi
- Department of Medical Sciences Clinical Physiology, Uppsala University, Uppsala, Sweden
| | - Marco Caminati
- Asthma, Allergy and Clinical Immunology Section, Department of Medicine, University of Verona, Verona, Italy
| | - Adeyinka Odebode
- Department of Basic Science, Kampala International University, Kampala, Uganda
| | | | - Davide Paolo Caimmi
- IDESP, University of Montpellier and INSERM, Montpellier, France.,Departement of Pneumology, University Hospital of Montpellier, Montpellier, France
| | - Carole Cassagne
- VITROME, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Pascal Demoly
- IDESP, University of Montpellier and INSERM, Montpellier, France.,Departement of Pneumology, University Hospital of Montpellier, Montpellier, France
| | - Enrico Heffler
- Personalized Medicine, Asthma and Allergy Humanitas Clinical and Research Center IRCCS Rozzano, Rozzano, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Estelle Menu
- VITROME, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Bright I Nwaru
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Youssouf Sereme
- MEPHI, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France.,Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
| | - Stéphane Ranque
- VITROME, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Monika Raulf
- Department of Allergology and Immunology, Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-Universität Bochum (IPA), Bochum, Germany
| | - Wojciech Feleszko
- Department of Pediatric Pulmonology and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Christer Janson
- Department of Medical Sciences Respiratory, Allergy and Sleep Research, Uppsala University, Uppsala, Sweden
| | - Carmen Galán
- International Campus of Excellence on Agrifood (ceiA3), University of Cordoba, Córdoba, Spain.,Andalusian Inter-University Institute for Earth System Research (IISTA), University of Cordoba, Córdoba, Spain
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207
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Strategies for improving hydrolytic efficiency of crude multienzyme extracts in mushroom processing. Heliyon 2022; 8:e11312. [DOI: 10.1016/j.heliyon.2022.e11312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/24/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
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208
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Tedersoo L, Mikryukov V, Zizka A, Bahram M, Hagh‐Doust N, Anslan S, Prylutskyi O, Delgado‐Baquerizo M, Maestre FT, Pärn J, Öpik M, Moora M, Zobel M, Espenberg M, Mander Ü, Khalid AN, Corrales A, Agan A, Vasco‐Palacios A, Saitta A, Rinaldi AC, Verbeken A, Sulistyo BP, Tamgnoue B, Furneaux B, Ritter CD, Nyamukondiwa C, Sharp C, Marín C, Gohar D, Klavina D, Sharmah D, Dai DQ, Nouhra E, Biersma EM, Rähn E, Cameron E, De Crop E, Otsing E, Davydov EA, Albornoz F, Brearley FQ, Buegger F, Zahn G, Bonito G, Hiiesalu I, Barrio IC, Heilmann‐Clausen J, Ankuda J, Kupagme JY, Maciá‐Vicente JG, Fovo JD, Geml J, Alatalo JM, Alvarez‐Manjarrez J, Põldmaa K, Runnel K, Adamson K, Bråthen KA, Pritsch K, Tchan KI, Armolaitis K, Hyde KD, Newsham K, Panksep K, Lateef AA, Tiirmann L, Hansson L, Lamit LJ, Saba M, Tuomi M, Gryzenhout M, Bauters M, Piepenbring M, Wijayawardene N, Yorou NS, Kurina O, Mortimer PE, Meidl P, Kohout P, Nilsson RH, Puusepp R, Drenkhan R, Garibay‐Orijel R, Godoy R, Alkahtani S, Rahimlou S, Dudov SV, Põlme S, Ghosh S, Mundra S, Ahmed T, Netherway T, Henkel TW, Roslin T, Nteziryayo V, Fedosov VE, Onipchenko V, Yasanthika WAE, Lim YW, et alTedersoo L, Mikryukov V, Zizka A, Bahram M, Hagh‐Doust N, Anslan S, Prylutskyi O, Delgado‐Baquerizo M, Maestre FT, Pärn J, Öpik M, Moora M, Zobel M, Espenberg M, Mander Ü, Khalid AN, Corrales A, Agan A, Vasco‐Palacios A, Saitta A, Rinaldi AC, Verbeken A, Sulistyo BP, Tamgnoue B, Furneaux B, Ritter CD, Nyamukondiwa C, Sharp C, Marín C, Gohar D, Klavina D, Sharmah D, Dai DQ, Nouhra E, Biersma EM, Rähn E, Cameron E, De Crop E, Otsing E, Davydov EA, Albornoz F, Brearley FQ, Buegger F, Zahn G, Bonito G, Hiiesalu I, Barrio IC, Heilmann‐Clausen J, Ankuda J, Kupagme JY, Maciá‐Vicente JG, Fovo JD, Geml J, Alatalo JM, Alvarez‐Manjarrez J, Põldmaa K, Runnel K, Adamson K, Bråthen KA, Pritsch K, Tchan KI, Armolaitis K, Hyde KD, Newsham K, Panksep K, Lateef AA, Tiirmann L, Hansson L, Lamit LJ, Saba M, Tuomi M, Gryzenhout M, Bauters M, Piepenbring M, Wijayawardene N, Yorou NS, Kurina O, Mortimer PE, Meidl P, Kohout P, Nilsson RH, Puusepp R, Drenkhan R, Garibay‐Orijel R, Godoy R, Alkahtani S, Rahimlou S, Dudov SV, Põlme S, Ghosh S, Mundra S, Ahmed T, Netherway T, Henkel TW, Roslin T, Nteziryayo V, Fedosov VE, Onipchenko V, Yasanthika WAE, Lim YW, Soudzilovskaia NA, Antonelli A, Kõljalg U, Abarenkov K. Global patterns in endemicity and vulnerability of soil fungi. GLOBAL CHANGE BIOLOGY 2022; 28:6696-6710. [PMID: 36056462 PMCID: PMC9826061 DOI: 10.1111/gcb.16398] [Show More Authors] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/09/2022] [Indexed: 05/29/2023]
Abstract
Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | | | | | - Mohammad Bahram
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Sten Anslan
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Oleh Prylutskyi
- Department of Mycology and Plant Resistance, School of BiologyV.N. Karazin Kharkiv National UniversityKharkivUkraine
| | - Manuel Delgado‐Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, and Unidad Asociada CSIC‐UPO (BioFun)Universidad Pablo de OlavideSevillaSpain
| | - Fernando T. Maestre
- Departamento de Ecología, Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’Universidad de AlicanteAlicanteSpain
| | - Jaan Pärn
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Maarja Öpik
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mari Moora
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Martin Zobel
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mikk Espenberg
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Ülo Mander
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | | | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología‐UR (CIMBIUR)Universidad del RosarioBogotáColombia
| | - Ahto Agan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Aída‐M. Vasco‐Palacios
- BioMicro, Escuela de MicrobiologíaUniversidad de Antioquia UdeAMedellinAntioquiaColombia
| | - Alessandro Saitta
- Department of Agricultural, Food and Forest SciencesUniversity of PalermoPalermoItaly
| | - Andrea C. Rinaldi
- Department of Biomedical SciencesUniversity of CagliariCagliariItaly
| | | | - Bobby P. Sulistyo
- Department of BiomedicineIndonesia International Institute for Life SciencesJakartaIndonesia
| | - Boris Tamgnoue
- Department of Crop ScienceUniversity of DschangDschangCameroon
| | - Brendan Furneaux
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | | | - Casper Nyamukondiwa
- Department of Biological Sciences and BiotechnologyBotswana International University of Science and TechnologyPalapyeBotswana
| | - Cathy Sharp
- Natural History Museum of ZimbabweBulawayoZimbabwe
| | - César Marín
- Centro de Investigación e Innovación para el Cambio Climático (CiiCC)Universidad SantoTomásSantiagoChile
| | - Daniyal Gohar
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Darta Klavina
- Latvian State Forest Research Insitute SilavaSalaspilsLatvia
| | - Dipon Sharmah
- Department of Botany, Jawaharlal Nehru Rajkeeya MahavidyalayaPondicherry UniversityPort BlairIndia
| | - Dong Qin Dai
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingChina
| | - Eduardo Nouhra
- Instituto Multidisciplinario de Biología Vegetal (CONICET)Universidad Nacional de CórdobaCordobaArgentina
| | | | - Elisabeth Rähn
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Erin K. Cameron
- Department of Environmental ScienceSaint Mary's UniversityHalifaxCanada
| | | | - Eveli Otsing
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | | | | | - Francis Q. Brearley
- Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
| | | | | | - Gregory Bonito
- Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Inga Hiiesalu
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Isabel C. Barrio
- Faculty of Natural and Environmental SciencesAgricultural University of IcelandHvanneyriIceland
| | | | - Jelena Ankuda
- Department of Silviculture and EcologyInstitute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC)GirionysLithuania
| | - John Y. Kupagme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Jose G. Maciá‐Vicente
- Plant Ecology and Nature ConservationWageningen University & ResearchWageningenThe Netherlands
| | | | - József Geml
- ELKH‐EKKE Lendület Environmental Microbiome Research GroupEszterházy Károly Catholic UniversityEgerHungary
| | | | | | - Kadri Põldmaa
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Kadri Runnel
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Kalev Adamson
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Kari Anne Bråthen
- Department of Arctic and Marine BiologyThe Arctic University of NorwayTromsøNorway
| | | | - Kassim I. Tchan
- Research Unit Tropical Mycology and Plants‐Soil Fungi InteractionsUniversity of ParakouParakouBenin
| | - Kęstutis Armolaitis
- Department of Silviculture and EcologyInstitute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC)GirionysLithuania
| | - Kevin D. Hyde
- Center of Excellence in Fungal ResearchMae Fah Luang UniversityChiang RaiThailand
| | | | - Kristel Panksep
- Chair of Hydrobiology and FisheryEstonian University of Life SciencesTartuEstonia
| | | | - Liis Tiirmann
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Linda Hansson
- Gothenburg Centre for Sustainable DevelopmentGothenburgSweden
| | - Louis J. Lamit
- Department of BiologySyracuse UniversitySyracuseNew YorkUSA
- Department of Environmental and Forest BiologyState University of New York College of Environmental Science and ForestrySyracuseNew YorkUSA
| | - Malka Saba
- Department of Plant SciencesQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Maria Tuomi
- Department of Arctic and Marine BiologyThe Arctic University of NorwayTromsøNorway
| | - Marieka Gryzenhout
- Department of GeneticsUniversity of the Free StateBloemfonteinSouth Africa
| | | | - Meike Piepenbring
- Mycology Working GroupGoethe University Frankfurt am MainFrankfurt am MainGermany
| | - Nalin Wijayawardene
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingChina
| | - Nourou S. Yorou
- Research Unit Tropical Mycology and Plants‐Soil Fungi InteractionsUniversity of ParakouParakouBenin
| | - Olavi Kurina
- Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartuEstonia
| | - Peter E. Mortimer
- Center For Mountain Futures, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Peter Meidl
- Institut für BiologieFreie Universität BerlinBerlinGermany
| | - Petr Kohout
- Institute of MicrobiologyCzech Academy of SciencesPragueCzech Republic
| | - Rolf Henrik Nilsson
- Gothenburg Global Biodiversity CentreUniversity of GothenburgGothenburgSweden
| | - Rasmus Puusepp
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Rein Drenkhan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | | | - Roberto Godoy
- Instituto Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Saad Alkahtani
- College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Saleh Rahimlou
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Sergey V. Dudov
- Department of Ecology and Plant GeographyMoscow Lomonosov State UniversityMoscowRussia
| | - Sergei Põlme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Soumya Ghosh
- Department of GeneticsUniversity of the Free StateBloemfonteinSouth Africa
| | - Sunil Mundra
- Department of Biology, College of ScienceUnited Arab Emirates UniversityAbu DhabiUAE
| | - Talaat Ahmed
- Environmental Science CenterQatar UniversityDohaQatar
| | - Tarquin Netherway
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Terry W. Henkel
- Department of Biological SciencesCalifornia State Polytechnic UniversityArcataCaliforniaUSA
| | - Tomas Roslin
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Vincent Nteziryayo
- Department of Food Science and TechnologyUniversity of BurundiBujumburaBurundi
| | - Vladimir E. Fedosov
- Department of Ecology and Plant GeographyMoscow Lomonosov State UniversityMoscowRussia
| | | | | | - Young Woon Lim
- School of Biological Sciences and Institute of MicrobiologySeoul National UniversitySeoulSouth Korea
| | | | | | - Urmas Kõljalg
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
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209
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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: 1.0] [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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210
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Kim D, Gilchrist CLM, Chun J, Steinegger M. UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. Nucleic Acids Res 2022; 51:D777-D784. [PMID: 36271795 PMCID: PMC9825530 DOI: 10.1093/nar/gkac894] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/13/2022] [Accepted: 10/04/2022] [Indexed: 01/30/2023] Open
Abstract
In phylogenomics the evolutionary relationship of organisms is studied by their genomic information. A common approach to phylogenomics is to extract related genes from each organism, build a multiple sequence alignment and then reconstruct evolution relations through a phylogenetic tree. Often a set of highly conserved genes occurring in single-copy, called core genes, are used for this analysis, as they allow efficient automation within a taxonomic clade. Here we introduce the Universal Fungal Core Genes (UFCG) database and pipeline for genome-wide phylogenetic analysis of fungi. The UFCG database consists of 61 curated fungal marker genes, including a novel set of 41 computationally derived core genes and 20 canonical genes derived from literature, as well as marker gene sequences extracted from publicly available fungal genomes. Furthermore, we provide an easy-to-use, fully automated and open-source pipeline for marker gene extraction, training and phylogenetic tree reconstruction. The UFCG pipeline can identify marker genes from genomic, proteomic and transcriptomic data, while producing phylogenies consistent with those previously reported, and is publicly available together with the UFCG database at https://ufcg.steineggerlab.com.
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Affiliation(s)
- Dongwook Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Cameron L M Gilchrist
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongsik Chun
- Correspondence may also be addressed to Jongsik Chun. Tel: +82 2 880 8153;
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211
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Ye K, Ai HL. Pimarane Diterpenes from Fungi. Pharmaceuticals (Basel) 2022; 15:ph15101291. [PMID: 36297402 PMCID: PMC9609704 DOI: 10.3390/ph15101291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Pimarane diterpenes are a kind of tricyclic diterpene, generally isolated from plant and fungi. In nature, fungi distribute widely and there are nearly two to three million species. They provide many secondary metabolites, including pimarane diterpenes, with novel skeletons and bioactivities. These natural products from fungi have the potential to be developed into clinical medicines. Herein, the structures and bioactivities of 197 pimarane diterpenes are summarized and the biosynthesis and pharmacological researches of pimarane diterpenes are introduced. This review may be useful improving the understanding of pimarane diterpenes from fungi.
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212
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Adam C, Magdalena Ś. Species Diversity of Mycoplankton on the Background of Selected Indicators of Water Quality in Stratified Mesotrophic Lakes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192013298. [PMID: 36293879 PMCID: PMC9602596 DOI: 10.3390/ijerph192013298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 06/08/2023]
Abstract
The aim of the study was to determine mycoplankton species diversity in relation to the physico-chemical parameters of lake waters. The research was carried out in the summer months in 15 mesotrophic lakes and showed a high ecological significance index for Rhodotorula glutinis, Epicoccum nigrum, Fusarium sporotrichioides, and Trichophyton violaceum. Mycoplankton abundance and species diversity decreased with the depth of water, which coincided with a decrease in oxygen content and organic matter concentration. A high concentration of nitrogen compounds (total nitrogen-TN and dissolved nitrogen-DN) limited the development of mycobiota in the hypolimnion. In the metalimnion, the intensive development of organisms, especially bacteria, limited mycoplankton abundance despite perfect physical and chemical conditions for its development. Finally, mycoplankton functioned the best in slightly alkaline waters.
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Affiliation(s)
- Cudowski Adam
- Department of Water Ecology, Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland
| | - Świsłocka Magdalena
- Department of Zoology and Genetics, Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland
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213
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Reyes EY, Shinohara ML. Host immune responses in the central nervous system during fungal infections. Immunol Rev 2022; 311:50-74. [PMID: 35672656 PMCID: PMC9489659 DOI: 10.1111/imr.13101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/24/2022] [Accepted: 05/18/2022] [Indexed: 12/19/2023]
Abstract
Fungal infections in the central nervous system (CNS) cause high morbidity and mortality. The frequency of CNS mycosis has increased over the last two decades as more individuals go through immunocompromised conditions for various reasons. Nevertheless, options for clinical interventions for CNS mycoses are still limited. Thus, there is an urgent need to understand the host-pathogen interaction mechanisms in CNS mycoses for developing novel treatments. Although the CNS has been regarded as an immune-privileged site, recent studies demonstrate the critical involvement of immune responses elicited by CNS-resident and CNS-infiltrated cells during fungal infections. In this review, we discuss mechanisms of fungal invasion in the CNS, fungal pathogen detection by CNS-resident cells (microglia, astrocytes, oligodendrocytes, neurons), roles of CNS-infiltrated leukocytes, and host immune responses. We consider that understanding host immune responses in the CNS is crucial for endeavors to develop treatments for CNS mycosis.
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Affiliation(s)
- Estefany Y. Reyes
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Mari L. Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27705, USA
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214
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Voglmayr H, Schertler A, Essl F, Krisai-Greilhuber I. Alien and cryptogenic fungi and oomycetes in Austria: an annotated checklist (2nd edition). Biol Invasions 2022; 25:27-38. [PMID: 36643959 PMCID: PMC9832105 DOI: 10.1007/s10530-022-02896-2] [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: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 01/18/2023]
Abstract
Fungal invasions can have far-reaching consequences, and despite increasing relevance, fungi are notoriously underrepresented in invasion science. Here, we present the second annotated checklist for alien and cryptogenic fungi and oomycetes in Austria. This list contains 375 taxa of which 278 are classified as established; compared to the first checklist from 2002, this amounts to an almost five-fold increase and the number of decade-wise first records is steadily rising since the mid-twentieth century. The introduction pathway is unclear for the vast majority of taxa, while the main means of spread within the country is unassisted secondary spread. Fungi were predominantly introduced from the Northern Hemisphere, especially North America and Temperate Asia. Rates of newly recorded alien fungi differ among phyla; the majority belongs to the Ascomycota, which experienced an 9.6-fold increase in numbers. Orders found most frequently are powdery mildews (Erysiphales, Ascomycota), downy mildews (Peronosporales, Oomycota), agarics (Agaricales, Basidiomycota), Mycosphaerellales (Ascomycota), rusts (Pucciniales, Basidiomycota) and Pleosporales (Ascomycota). The majority (about 80%) of the taxa are plant pathogens, while animal pathogens are few but severely affecting their native hosts. The dominance of pathogens in our checklist underlines the need of better tackling fungal invasions-especially in the light of emerging infectious diseases-and highlights potential knowledge gaps for ectomycorrhizal and saprobic alien fungi, whose invasion processes are often much more inconspicuous. Our results show that fungal invasions are a phenomenon of increasing importance, and collaborative efforts are needed for advancing the knowledge and management of this important group. Supplementary Information The online version contains supplementary material available at 10.1007/s10530-022-02896-2.
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Affiliation(s)
- Hermann Voglmayr
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Anna Schertler
- BioInvasions, Global Change, Macroecology-Group, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Franz Essl
- BioInvasions, Global Change, Macroecology-Group, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Irmgard Krisai-Greilhuber
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
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215
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Cho M, Kwon SL, Heo YM, Lee YM, Lee H, Kim C, Ahn BJ, Kim JJ. Seven Unrecorded Indigenous Fungi from Mudeungsan National Park in Korea. MYCOBIOLOGY 2022; 50:203-212. [PMID: 36158043 PMCID: PMC9467549 DOI: 10.1080/12298093.2022.2109269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/13/2022] [Accepted: 07/31/2022] [Indexed: 06/16/2023]
Abstract
Fungi act as important decomposers in the forest environment. They recycle essential nutrients, promote plant growth through mycorrhizal relationships, and act as food for small animals. Samples of 265 indigenous fungal species were collected from Mudeungsan National Park in 2020. These species were identified based on morphological, molecular, and phylogenetic analyses using the internal transcribed spacer (ITS), nuclear large subunit rRNA (LSU), and RNA polymerase II second largest subunit (rpb2) regions. Subsequently, seven species were identified as unrecorded species in Korea: Cordyceps cicadae, Dentocorticium bicolor, Hymenochaete nanospora, Physisporinus crataegi, Rigidoporus piceicola, Russula raoultii, and Scutellinia crinita. This study reveals their detailed macro- and microscopic morphological characteristics with phylogenetic trees to report them as unrecorded species in Korea.
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Affiliation(s)
- Minseo Cho
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Sun Lul Kwon
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | | | - Young Min Lee
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Hanbyul Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Changmu Kim
- Division of Biological and Genetic Resources Assessment, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Byoung Jun Ahn
- Department of Forest Products and Industry, Division of Forest Industrial Materials, National Institute of Forest Science, Seoul, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
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216
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Richter F, Bindschedler S, Calonne-Salmon M, Declerck S, Junier P, Stanley CE. Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi. FEMS Microbiol Rev 2022; 46:6674677. [PMID: 36001464 PMCID: PMC9779915 DOI: 10.1093/femsre/fuac039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 01/07/2023] Open
Abstract
This review highlights new advances in the emerging field of 'Fungi-on-a-Chip' microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.
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Affiliation(s)
- Felix Richter
- Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Corresponding author: Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, United Kingdom. E-mail:
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217
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Oke MA, Afolabi FJ, Oyeleke OO, Kilani TA, Adeosun AR, Olanbiwoninu AA, Adebayo EA. Ganoderma lucidum: Unutilized natural medicine and promising future solution to emerging diseases in Africa. Front Pharmacol 2022; 13:952027. [PMID: 36071846 PMCID: PMC9441938 DOI: 10.3389/fphar.2022.952027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/04/2022] [Indexed: 11/18/2022] Open
Abstract
Ganoderma lucidum is a well-known medicinal mushroom that has been used for the prevention and treatment of different ailments to enhance longevity and health specifically in China, Japan, and Korea. It was known as "God's herb" in ancient China as it was believed to prolong life, enhance the youthful spirit and sustain/preserve vitality. G. lucidum is seldom collected from nature and is substantially cultivated on wood logs and sawdust in plastic bags or bottles to meet the international market demand. Both in vitro and in vivo studies on the copious metabolic activities of G. lucidum have been carried out. Varied groups of chemical compounds including triterpenoids, polysaccharides, proteins, amino acids, nucleosides, alkaloids, steroids, lactones, lectins, fatty acids, and enzymes with potent pharmacological activities have been isolated from the mycelia and fruiting bodies of G. lucidum. Several researchers have reported the abundance and diversification of its biological actions triggered by these chemical compounds. Triterpenoids and polysaccharides of G. lucidum have been reported to possess cytotoxic, hepatoprotective, antihypertensive, hypocholesterolemic, antihistaminic effects, antioxidant, antimicrobial, anti-inflammatory, hypoglycemic antiallergic, neuroprotective, antitumor, immunomodulatory and antiangiogenic activities. Various formulations have been developed, patented, and utilized as nutraceuticals, cosmeceuticals, and pharmaceuticals from G. lucidum extracts and active compounds. Thus, this review presents current updates on emerging infectious diseases and highlights the scope, dynamics, and advances in infectious disease management with a particular focus on Ganoderma lucidum, an unutilized natural medicine as a promising future solution to emerging diseases in Africa. However, details such as the chemical compound and mode of action of each bioactive against different emerging diseases were not discussed in this study.
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Affiliation(s)
- M. A. Oke
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Microbiology and Nanobiotechnology Laboratory, LAUTECH, Ogbomoso, Nigeria
| | - F. J. Afolabi
- Mushrooms Department, National Biotechnology Development Centre, Ogbomoso, Nigeria
| | - O. O. Oyeleke
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Microbiology and Nanobiotechnology Laboratory, LAUTECH, Ogbomoso, Nigeria
| | - T. A. Kilani
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Microbiology and Nanobiotechnology Laboratory, LAUTECH, Ogbomoso, Nigeria
| | - A. R. Adeosun
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Microbiology and Nanobiotechnology Laboratory, LAUTECH, Ogbomoso, Nigeria
| | - A. A. Olanbiwoninu
- Department of Biological Sciences, Ajayi Crowther University, Oyo, Nigeria
| | - E. A. Adebayo
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Microbiology and Nanobiotechnology Laboratory, LAUTECH, Ogbomoso, Nigeria
- Mushrooms Department, National Biotechnology Development Centre, Ogbomoso, Nigeria
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218
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Sahu SR, Bose S, Singh M, Kumari P, Dutta A, Utkalaja BG, Patel SK, Acharya N. Vaccines against candidiasis: Status, challenges and emerging opportunity. Front Cell Infect Microbiol 2022; 12:1002406. [PMID: 36061876 PMCID: PMC9433539 DOI: 10.3389/fcimb.2022.1002406] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Candidiasis is a mycosis caused by opportunistic Candida species. The occurrence of fungal infections has considerably increased in the last few years primarily due to an increase in the number of immune-suppressed individuals. Alarming bloodstream infections due to Candida sp. are associated with a higher rate of morbidity and mortality, and are emerged as major healthcare concerns worldwide. Currently, chemotherapy is the sole available option for combating fungal diseases. Moreover, the emergence of resistance to these limited available anti-fungal drugs has further accentuated the concern and highlighted the need for early detection of fungal infections, identification of novel antifungal drug targets, and development of effective therapeutics and prophylactics. Thus, there is an increasing interest in developing safe and potent immune-based therapeutics to tackle fungal diseases. In this context, vaccine design and its development have a priority. Nonetheless, despite significant advances in immune and vaccine biology over time, a viable commercialized vaccine remains awaited against fungal infections. In this minireview, we enumerate various concerted efforts made till date towards the development of anti-Candida vaccines, an option with pan-fugal vaccine, vaccines in the clinical trial, challenges, and future opportunities.
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Affiliation(s)
- Satya Ranjan Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional center of Biotechnology, Faridabad, India
| | - Swagata Bose
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | - Manish Singh
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Premlata Kumari
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional center of Biotechnology, Faridabad, India
| | - Abinash Dutta
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Bhabasha Gyanadeep Utkalaja
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional center of Biotechnology, Faridabad, India
| | - Shraddheya Kumar Patel
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional center of Biotechnology, Faridabad, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- *Correspondence: Narottam Acharya, ;
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219
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Knowles SL, Raja HA, Roberts CD, Oberlies NH. Fungal-fungal co-culture: a primer for generating chemical diversity. Nat Prod Rep 2022; 39:1557-1573. [PMID: 35137758 PMCID: PMC9384855 DOI: 10.1039/d1np00070e] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Indexed: 01/25/2023]
Abstract
Covering: 2002 to 2020In their natural environment, fungi must compete for resources. It has been hypothesized that this competition likely induces the biosynthesis of secondary metabolites for defence. In a quest to discover new chemical diversity from fungal cultures, a growing trend has been to recapitulate this competitive environment in the laboratory, essentially growing fungi in co-culture. This review covers fungal-fungal co-culture studies beginning with the first literature report in 2002. Since then, there has been a growing number of new secondary metabolites reported as a result of fungal co-culture studies. Specifically, this review discusses and provides insights into (1) rationale for pairing fungal strains, (2) ways to grow fungi for co-culture, (3) different approaches to screening fungal co-cultures for chemical diversity, (4) determining the secondary metabolite-producing strain, and (5) final thoughts regarding the fungal-fungal co-culture approach. Our goal is to provide a set of practical strategies for fungal co-culture studies to generate unique chemical diversity that the natural products research community can utilize.
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Affiliation(s)
- Sonja L Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Christopher D Roberts
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
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220
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Automatic Mushroom Species Classification Model for Foodborne Disease Prevention Based on Vision Transformer. J FOOD QUALITY 2022. [DOI: 10.1155/2022/1173102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Mushrooms are the fleshy, spore-bearing structure of certain fungi, produced by a group of mycelia and buried in a substratum. Mushrooms are classified as edible, medicinal, and poisonous. However, many poisoning incidents occur yearly by consuming wild mushrooms. Thousands of poisoning incidents are reported each year globally, and 80% of these are from unidentified species of mushrooms. Mushroom poisoning is one of the most serious food safety issues worldwide. Motivated by this problem, this study uses an open-source mushroom dataset and employs several data augmentation approaches to decrease the probability of model overfitting. We propose a novel deep learning pipeline (ViT-Mushroom) for mushroom classification using the Vision Transformer large network (ViT-L/32). We compared the performance of our method against that of a convolutional neural network (CNN). We visualized the high-dimensional outputs of the ViT-L/32 model to achieve the interpretability of ViT-L/32 using the t-distributed stochastic neighbor embedding (t-SNE) method. The results show that ViT-L/32 is the best on the testing dataset, with an accuracy score of 95.97%. These results surpass previous approaches in reducing intraclass variability and generating well-separated feature embeddings. The proposed method is a promising deep learning model capable of automatically classifying mushroom species, helping wild mushroom consumers avoid eating toxic mushrooms, safeguarding food safety, and preventing public health incidents of food poisoning. The results will offer valuable resources for food scientists, nutritionists, and the public health sector regarding the safety and quality of mushrooms.
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221
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Wijayawardene NN, Dai DQ, Zhu ML, Wanasinghe DN, Kumla J, Zhang GQ, Zhang TT, Han LS, Tibpromma S, Chen HH. Fungi associated with dead branches of Magnolia grandiflora: A case study from Qujing, China. Front Microbiol 2022; 13:954680. [PMID: 35992688 PMCID: PMC9386272 DOI: 10.3389/fmicb.2022.954680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
As a result of an ongoing survey of microfungi associated with garden and ornamental plants in Qijing, Yunnan, China, several saprobic fungal taxa were isolated from Magnolia grandiflora. Both morphological and combined SSU, LSU, ITS, tef1, and rpb2 locus phylogenetic analyses (maximum-likelihood and Bayesian analyses) were carried out to identify the fungal taxa. Three new species are introduced in Pleosporales, viz., Lonicericola qujingensis (Parabambusicolaceae), Phragmocamarosporium magnoliae, and Periacma qujingensis (Lentitheciaceae). Botryosphaeria dothidea, Diplodia mutila, and Diplodia seriata (in Botryosphaeriaceae) are reported from Magnolia grandiflora for the first time in China. Angustimassarina populi (Amorosiaceae) is reported for the first time on M. grandiflora from China, and this is the first report of a member of this genus outside Europe. Shearia formosa is also reported for the first time on M. grandiflora from China.
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Affiliation(s)
- Nalin N. Wijayawardene
- Center for Yunnan Plateau Biological Resources Protection and Utilization, Yunnan Engineering Research Center of Fruit Wine, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
- Section of Genetics, Institute for Research and Development in Health and Social Care, Battaramulla, Sri Lanka
| | - Dong-Qin Dai
- Center for Yunnan Plateau Biological Resources Protection and Utilization, Yunnan Engineering Research Center of Fruit Wine, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Mei-Ling Zhu
- Center for Yunnan Plateau Biological Resources Protection and Utilization, Yunnan Engineering Research Center of Fruit Wine, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Dhanushka N. Wanasinghe
- Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jaturong Kumla
- Research Centre of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Gui-Qing Zhang
- Center for Yunnan Plateau Biological Resources Protection and Utilization, Yunnan Engineering Research Center of Fruit Wine, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Ting-Ting Zhang
- Center for Yunnan Plateau Biological Resources Protection and Utilization, Yunnan Engineering Research Center of Fruit Wine, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Li-Su Han
- Center for Yunnan Plateau Biological Resources Protection and Utilization, Yunnan Engineering Research Center of Fruit Wine, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Saowaluck Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, Yunnan Engineering Research Center of Fruit Wine, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Huan-Huan Chen
- Center for Yunnan Plateau Biological Resources Protection and Utilization, Yunnan Engineering Research Center of Fruit Wine, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
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222
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Rivera-Chávez J, Ceapă CD, Figueroa M. Biological Dark Matter Exploration using Data Mining for the Discovery of Antimicrobial Natural Products. PLANTA MEDICA 2022; 88:702-720. [PMID: 35697058 DOI: 10.1055/a-1795-0562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The discovery of novel antimicrobials has significantly slowed down over the last three decades. At the same time, humans rely increasingly on antimicrobials because of the progressive antimicrobial resistance in medical practices, human communities, and the environment. Data mining is currently considered a promising option in the discovery of new antibiotics. Some of the advantages of data mining are the ability to predict chemical structures from sequence data, anticipation of the presence of novel metabolites, the understanding of gene evolution, and the corroboration of data from multiple omics technologies. This review analyzes the state-of-the-art for data mining in the fields of bacteria, fungi, and plant genomic data, as well as metabologenomics. It also summarizes some of the most recent research accomplishments in the field, all pinpointing to innovation through uncovering and implementing the next generation of antimicrobials.
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Affiliation(s)
- José Rivera-Chávez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Corina-Diana Ceapă
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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223
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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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224
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Babb-Biernacki SJ, Esselstyn JA, Doyle VP. Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont. J Fungi (Basel) 2022; 8:jof8080799. [PMID: 36012788 PMCID: PMC9409666 DOI: 10.3390/jof8080799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Far more biodiversity exists in Fungi than has been described, or could be described in several lifetimes, given current rates of species discovery. Although this problem is widespread taxonomically, our knowledge of animal-associated fungi is especially lacking. Fungi in the genus Pneumocystis are obligate inhabitants of mammal lungs, and they have been detected in a phylogenetically diverse array of species representing many major mammal lineages. The hypothesis that Pneumocystis cospeciate with their mammalian hosts suggests that thousands of Pneumocystis species may exist, potentially equal to the number of mammal species. However, only six species have been described, and the true correspondence of Pneumocystis diversity to host species boundaries is unclear. Here, we use molecular species delimitation to estimate the boundaries of Pneumocystis species sampled from 55 mammal species representing eight orders. Our results suggest that Pneumocystis species often colonize several closely related mammals, especially those in the same genus. Using the newly estimated ratio of fungal to host diversity, we estimate ≈4600 to 6250 Pneumocystis species inhabit the 6495 currently recognized extant mammal species. Additionally, we review the literature and find that only 240 (~3.7%) mammal species have been screened for Pneumocystis, and many detected Pneumocystis lineages are not represented by any genetic data. Although crude, our findings challenge the dominant perspective of strict specificity of Pneumocystis to their mammal hosts and highlight an abundance of undescribed diversity.
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Affiliation(s)
- Spenser J. Babb-Biernacki
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
- Correspondence:
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Vinson P. Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70809, USA;
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225
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Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years. J Fungi (Basel) 2022; 8:jof8080803. [PMID: 36012792 PMCID: PMC9410331 DOI: 10.3390/jof8080803] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
Fungi are amongst the most abundant and diverse organisms. Despite being widely known for their adverse role in food spoilage or as pathogens for humans, animals, or plants, they also present several beneficial effects. Fungi contribute to human well-being due to their role as decomposers, degrading decay matter into smaller molecules which can be easily used by other ecosystem members. These organisms can produce medicinal compounds or modulate protective immune responses in human intestine. Fungi intervene in diverse food processes or act as a food supply. Due to fungal diversity, the unequivocal identification of these organisms is crucial to increasing their practical applications and decreasing their adverse effects. The process of identification could be achieved through the integral sequencing of fungi genomes. However, this procedure would be time-consuming and rather cost-inefficient. Therefore, several molecular markers have been developed to overcome these limitations. The chronology of DNA-based molecular markers development can be divided into three main steps: (1) prior to the development of the PCR technique (RFLP); (2) after the development of the PCR technique (RAPD, AFLP, ISSR, VNTR, SNP, InDels, and DNA barcoding); (3) after the development of the massive parallel sequencing technique (Metabarcoding and WGS). Therefore, the present review covers an overview of the most recently developed molecular markers used for fungal detection and identification.
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226
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New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True? J Fungi (Basel) 2022; 8:jof8070737. [PMID: 35887492 PMCID: PMC9320658 DOI: 10.3390/jof8070737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as "What's in my soil?", to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.
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227
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Kirdeeva Y, Fedorova O, Daks A, Barlev N, Shuvalov O. How Should the Worldwide Knowledge of Traditional Cancer Healing Be Integrated with Herbs and Mushrooms into Modern Molecular Pharmacology? Pharmaceuticals (Basel) 2022; 15:868. [PMID: 35890166 PMCID: PMC9320176 DOI: 10.3390/ph15070868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 12/04/2022] Open
Abstract
Traditional herbal medicine (THM) is a "core" from which modern medicine has evolved over time. Besides this, one third of people worldwide have no access to modern medicine and rely only on traditional medicine. To date, drugs of plant origin, or their derivates (paclitaxel, vinblastine, vincristine, vinorelbine, etoposide, camptothecin, topotecan, irinotecan, and omacetaxine), are very important in the therapy of malignancies and they are included in most chemotherapeutic regimes. To date, 391,000 plant and 14,000 mushroom species exist. Their medical and biochemical capabilities have not been studied in detail. In this review, we systematized the information about plants and mushrooms, as well as their active compounds with antitumor properties. Plants and mushrooms are divided based on the regions where they are used in ethnomedicine to treat malignancies. The majority of their active compounds with antineoplastic properties and mechanisms of action are described. Furthermore, on the basis of the available information, we divided them into two priority groups for research and for their potential of use in antitumor therapy. As there are many prerequisites and some examples how THM helps and strengthens modern medicine, finally, we discuss the positive points of THM and the management required to transform and integrate THM into the modern medicine practice.
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Affiliation(s)
- Yulia Kirdeeva
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (Y.K.); (O.F.); (A.D.)
| | - Olga Fedorova
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (Y.K.); (O.F.); (A.D.)
| | - Alexandra Daks
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (Y.K.); (O.F.); (A.D.)
| | - Nikolai Barlev
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (Y.K.); (O.F.); (A.D.)
- Orekhovich Institute of Biomedical Chemistry, 119435 Moscow, Russia
| | - Oleg Shuvalov
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (Y.K.); (O.F.); (A.D.)
- Orekhovich Institute of Biomedical Chemistry, 119435 Moscow, Russia
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228
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Zhao H, Zhou M, Liu XY, Wu F, Dai YC. Phylogeny, Divergence Time Estimation and Biogeography of the Genus Onnia (Basidiomycota, Hymenochaetaceae). Front Microbiol 2022; 13:907961. [PMID: 35875515 PMCID: PMC9301299 DOI: 10.3389/fmicb.2022.907961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Species of Onnia are important tree pathogens and play a crucial role in forest ecosystems. The species diversity and distribution of Onnia have been studied, however, its evolutionary history is poorly understood. In this study, we reconstructed the phylogeny of Onnia using internal transcribed spacers (ITS) and large subunit (LSU) rDNA sequence data. Molecular clock analyses developed the divergence times of Onnia based on a dataset (ITS + LSU rDNA + rpb1 + rpb2 + tef1α). Reconstruct Ancestral State in Phylogenies (RASP) was used to reconstruct the historical biogeography for the genus Onnia with a Dispersal Extinction Cladogenesis (DEC) model. Here, we provide a robust phylogeny of Onnia, with a description of a new species, Onnia himalayana from Yunnan Province, China. Molecular clock analyses suggested that the common ancestor of Onnia and Porodaedalea emerged in the Paleogene period with full support and a mean stem age of 56.9 Mya (95% highest posterior density of 35.9-81.6 Mya), and most species occurred in the Neogene period. Biogeographic studies suggest that Asia, especially in the Hengduan-Himalayan region, is probably the ancestral area. Five dispersals and two vicariances indicate that species of Onnia were rapidly diversified. Speciation occurred in the Old World and New World due to geographic separation. This study is the first inference of the divergence times, biogeography, and speciation of the genus Onnia.
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Affiliation(s)
- Heng Zhao
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Meng Zhou
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Fang Wu
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Yu-Cheng Dai
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
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Chen Y, Tian W, Guo Y, Madrid H, Maharachchikumbura SSN. Synhelminthosporium gen. et sp. nov. and Two New Species of Helminthosporium (Massarinaceae, Pleosporales) from Sichuan Province, China. J Fungi (Basel) 2022; 8:jof8070712. [PMID: 35887467 PMCID: PMC9316862 DOI: 10.3390/jof8070712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 02/06/2023] Open
Abstract
Helminthosporium is a polyphyletic genus in Massarinaceae (Pleosporales). Species of Helminthosporium are characterized by having septate and erect conidiophores, acro-pleurogenous and distoseptate conidia with a ring-shaped scar at the base. During a survey of fungal diversity in Sichuan Province, China, six Helminthosporium-like isolates were collected from dead branches of unknown trees. Five barcodes, including ITS (ITS1-5.8S-ITS2), SSU, LSU, TEF1, and RPB2 were amplified and sequenced. Morphological examination and multi-locus phylogenetic analyses revealed two new Helminthosporium species (H. chengduense sp. nov., and H. chinense sp. nov.), a new genus (Synhelminthosporium gen. nov.) with a type species Synhelminthosporium synnematoferum sp. nov., and two known species (Helminthosporium submersum and H. velutinum) within Massarinaceae. The new genus Synhelminthosporium differs from the phylogenetically closest genus Helminthosporium by producing synnematous conidiophores. This work expands our understanding of the diversity of Helminthosporium-like taxa in Sichuan Province, China.
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Affiliation(s)
- Yanpeng Chen
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China; (Y.C.); (W.T.); (Y.G.)
| | - Wenhui Tian
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China; (Y.C.); (W.T.); (Y.G.)
| | - Yaobin Guo
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China; (Y.C.); (W.T.); (Y.G.)
| | - Hugo Madrid
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Sede Iquique, Av. Luis Emilio Recabarren 2477, Iquique 1100000, Chile;
| | - Sajeewa S. N. Maharachchikumbura
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China; (Y.C.); (W.T.); (Y.G.)
- Correspondence: or
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230
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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: 4.3] [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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Chaudhary VB, Holland EP, Charman-Anderson S, Guzman A, Bell-Dereske L, Cheeke TE, Corrales A, Duchicela J, Egan C, Gupta MM, Hannula SE, Hestrin R, Hoosein S, Kumar A, Mhretu G, Neuenkamp L, Soti P, Xie Y, Helgason T. What are mycorrhizal traits? Trends Ecol Evol 2022; 37:573-581. [PMID: 35504748 DOI: 10.1016/j.tree.2022.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 12/29/2022]
Abstract
Traits are inherent properties of organisms, but how are they defined for organismal networks such as mycorrhizal symbioses? Mycorrhizal symbioses are complex and diverse belowground symbioses between plants and fungi that have proved challenging to fit into a unified and coherent trait framework. We propose an inclusive mycorrhizal trait framework that classifies traits as morphological, physiological, and phenological features that have functional implications for the symbiosis. We further classify mycorrhizal traits by location - plant, fungus, or the symbiosis - which highlights new questions in trait-based mycorrhizal ecology designed to charge and challenge the scientific community. This new framework is an opportunity for researchers to interrogate their data to identify novel insights and gaps in our understanding of mycorrhizal symbioses.
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Affiliation(s)
- V Bala Chaudhary
- Department of Environmental Studies, Dartmouth College, Hanover, NH 03755, USA.
| | | | | | - Aidee Guzman
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lukas Bell-Dereske
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Tanya E Cheeke
- School of Biological Sciences, Washington State University, Richland, WA 99354, USA
| | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 110151, Colombia
| | - Jessica Duchicela
- Departamento de Ciencias de la Vida, Universidad de las Fuerzas Armadas ESPE, Sangolquí 171103, Ecuador
| | - Cameron Egan
- Department of Biology, Okanagan College, 1000 KLO Rd, Kelowna, BC, Canada V1Y 4X8
| | - Manju M Gupta
- Department of Biology, University of Delhi, Sri Aurobindo College, Delhi 110017, India
| | - S Emilia Hannula
- Institute of Environmental Sciences, Leiden University, Leiden 2333, The Netherlands
| | - Rachel Hestrin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Shabana Hoosein
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO 80523, USA
| | - Amit Kumar
- Institute of Ecology, Faculty of Sustainability, Leuphana University of Lüneburg, 21335 Lüneburg, Germany
| | - Genet Mhretu
- Department of Biology, Mekelle University, Mekelle 231, Ethiopia
| | - Lena Neuenkamp
- University of Bern, Institute of Plant Sciences, Berne 3013, Switzerland; Department of Ecology and Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante 03009, Spain
| | - Pushpa Soti
- Biology Department, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Yichun Xie
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077
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232
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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: 1.3] [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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233
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Xiong X, Rao Y, Tu X, Wang Z, Gong J, Yang Y, Wu H, Liu X. Gut archaea associated with bacteria colonization and succession during piglet weaning transitions. BMC Vet Res 2022; 18:243. [PMID: 35751084 PMCID: PMC9229118 DOI: 10.1186/s12917-022-03330-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods. Results We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3. Conclusion Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03330-4.
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Affiliation(s)
- Xinwei Xiong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China.
| | - Yousheng Rao
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Xutang Tu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Zhangfeng Wang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Jishang Gong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Yanbei Yang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Haobin Wu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Xianxian Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, 330006, People's Republic of China.
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234
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Matsuoka S, Hatano Y, Osono T. Distribution and functional data of fungal families. Ecol Res 2022. [DOI: 10.1111/1440-1703.12315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shunsuke Matsuoka
- Graduate School of Information Science University of Hyogo Kobe Japan
| | - Yuki Hatano
- Graduate School of Science and Engineering Doshisha University Kyoto Japan
| | - Takashi Osono
- Faculty of Science and Engineering Doshisha University Kyoto Japan
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235
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O'Donnell K, Whitaker BK, Laraba I, Proctor RH, Brown DW, Broders K, Kim HS, McCormick SP, Busman M, Aoki T, Torres-Cruz TJ, Geiser DM. DNA Sequence-Based Identification of Fusarium: A Work in Progress. PLANT DISEASE 2022; 106:1597-1609. [PMID: 34907805 DOI: 10.1094/pdis-09-21-2035-sr] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent's identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists that need to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise more than 400 phylogenetically distinct species (i.e., phylospecies), with more than 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (FUSARIUM-ID v.3.0 and the nonredundant National Center for Biotechnology Information nucleotide collection that includes GenBank) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1, and RPB2) that resolve at or near the species level in every Fusarium species. The objectives of this Special Report, and its companion in this issue (Torres-Cruz et al. 2022), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.
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Affiliation(s)
- Kerry O'Donnell
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Briana K Whitaker
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Imane Laraba
- Oak Ridge Institute for Science and Education Fellow, Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Peoria, IL 61604, U.S.A
| | - Robert H Proctor
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Daren W Brown
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Kirk Broders
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Hye-Seon Kim
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Susan P McCormick
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Mark Busman
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Takayuki Aoki
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Terry J Torres-Cruz
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - David M Geiser
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
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236
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Porter DL, Naleway SE. Hyphal systems and their effect on the mechanical properties of fungal sporocarps. Acta Biomater 2022; 145:272-282. [PMID: 35421618 DOI: 10.1016/j.actbio.2022.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/01/2022]
Abstract
Little is known about the mechanical and material properties of hyphae, the single constituent material of Agaricomycetes fungi, despite a growing interest in fungus-based materials. In the Agaricomycetes (the mushrooms and allies), there are three types of hyphae that make up sporocarps: generative, skeletal, and ligative. All filamentous Agaricomycetes can be categorized into one of three categories of hyphal systems that compose them: monomitic, dimitic, and trimitic. Monomitic systems have only generative hyphae. Dimitic systems have generative and either skeletal (most common) or ligative. Trimitic systems are composed of all three kinds of hyphae. SEM imaging, compression testing, and theoretical modeling were used to characterize the material and mechanical properties of representative monomitic, dimitic, and trimitic sporocarps. Compression testing revealed an increase in the compression modulus and compressive strength with the addition of more hyphal types (monomitic to dimitic and dimitic to trimitic). The mesostructure of the trimitic sporocarp was tested and modeled, suggesting that the difference in properties between the solid material and the microtubule mesostructure is a result of differences in structure and not material. Theoretical modeling was completed to estimate the mechanical properties of the individual types of hyphae and showed that skeletal hyphae make the largest contribution to mechanical properties of fungal sporocarps. Understanding the contributions of the different types of hyphae may help in the design and application of fungi-based or bioinspired materials. STATEMENT OF SIGNIFICANCE: This research studies the material and mechanical properties of fungal sporocarps and their hyphae, the single constituent material of Agaricomycetes fungi. Though some work has been done on fungal hyphae, this research studies hyphae in context of the three hyphal systems found in Agaricomycetes fungi and estimates the properties of the hyphal filaments, which has not been done previously. This characterization was performed by analyzing the structures and mechanical properties of fungal sporocarps and calculating the theoretical mechanical properties of their hyphae. This data and the resulting conclusions may lead to a better design and implementation process of fungi-based materials in various applications using the properties now known or calculated.
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237
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Lobo-Moreira AB, Xavier-Santos S, Damacena-Silva L, Caramori SS. Trends on Microalgae-Fungi Consortia Research: An Alternative for Biofuel Production? Front Microbiol 2022; 13:903737. [PMID: 35722292 PMCID: PMC9199376 DOI: 10.3389/fmicb.2022.903737] [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: 03/24/2022] [Accepted: 04/11/2022] [Indexed: 11/26/2022] Open
Abstract
The utilization of microalgae and fungi on an industrial scale is a challenge for researchers. Based on the question “how fungi have contributed to microalgae research?,” we verified the scientific trends on microalgae-fungi consortia focused on biofuels production by searching for articles on the Web of Science and Scopus databases through the terms “microalgae*” or phytoplankton and “fung*.” We found 1,452 articles published between 1950 and 2020; since 2006, the publication numbers have increased rapidly. The articles were published in 12 languages, but most were written in English (96.3%). Among 72 countries, China (360 articles), USA (344), and Germany (155) led the publication rank. Among the 10 most-prolific authors, 8 were Chinese, like 5 of the most-productive institutions, whereas the National Cheng Kung University was on the top of the list. The sources that published the most on the subject were: Bioresource Technology (96), PLoS ONE (28), and Science of the Total Environment (26). The keyword analysis emphasized the magnitude of applications in microalgae-fungi consortia research. Confirming this research question, biofuels appeared as a research trend, especially biodiesel, biogas, and related terms like lipid, lipid accumulation, anaerobic digestion, and biogas upgrading. For 70 years, articles have been published, where China and the United States seem to dominate the research scenario, and biodiesel is the main biofuel derived from this consortium. However, microalgae-based biofuel biorefinery is still a bottleneck on an industrial scale. Recent environmental challenges, such as greenhouse gas mitigation, can be a promising field for that microalgae-fungi application.
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Affiliation(s)
- Ana Beatriz Lobo-Moreira
- Post Graduate Program in Natural Resources of Cerrado, State University of Goiás, Anápolis, Brazil
- *Correspondence: Ana Beatriz Lobo-Moreira
| | - Solange Xavier-Santos
- Laboratory of Basic, Applied and Mycology and Scientific Dissemination (FungiLab), State University of Goiás, Anápolis, Brazil
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238
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Aman N, Khalid AN, Moncalvo JM. A compendium of macrofungi of Pakistan by ecoregions. MycoKeys 2022; 89:171-233. [PMID: 36760828 PMCID: PMC9849087 DOI: 10.3897/mycokeys.89.81148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/25/2022] [Indexed: 11/12/2022] Open
Abstract
Macrofungi form fruiting bodies that can be detected with the naked eye in the field and handled by hand. They mostly consist of basidiomycetes, but also include some ascomycetes. Mycology in Pakistan is still in its infancy, but there have been many historical reports and checklists of macrofungi occurrence from its 15 ecoregions, which range from Himalayan alpine grasslands and subtropical pine forests to deserts and xeric shrublands. In this work, we searched and reviewed the historical literature and the GenBank database for compiling a comprehensive list of macrofungi reported from Pakistan to date. We recorded 1,293 species belonging to 411 genera, 115 families and 24 orders. These occurrences were updated taxonomically following the classification system currently proposed in the Index Fungorum website. The highest represented order by taxon number is Agaricales (47%) with 31 families, 146 genera and 602 species, followed by Polyporales (11%), Russulales (9%) and Pezizales (8%). Genera occurrence reported therein are presented for each ecoregion to the best of our ability given the data. We also discussed the currently known macrofungi diversity between different ecoregions in Pakistan. Overall, this work should serve as a solid foundation for the inclusion of Pakistan macrofungi in global biodiversity and conservation studies.
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Affiliation(s)
- Nourin Aman
- Department of Botany, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, PakistanUniversity of the PunjabLahorePakistan
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario M5S 2C6, CanadaDepartment of Natural History, Royal Ontario MuseumTorontoCanada
| | - Abdul Nasir Khalid
- Department of Botany, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, PakistanUniversity of the PunjabLahorePakistan
| | - Jean-Marc Moncalvo
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario M5S 2C6, CanadaDepartment of Natural History, Royal Ontario MuseumTorontoCanada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Ontario M5S 3B2, CanadaUniversity of TorontoTorontoCanada
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239
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Xu KX, Shan XN, Ruan Y, Deng J, Wang L. Three new Penicillium species isolated from the tidal flats of China. PeerJ 2022; 10:e13224. [PMID: 35547185 PMCID: PMC9083529 DOI: 10.7717/peerj.13224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/14/2022] [Indexed: 01/12/2023] Open
Abstract
During a survey of culturable fungi in the coastal areas of China, three new species of Penicillium sect. Lanata-Divaricata were discovered and studied with a polyphasic taxonomic approach, and then named as P. donggangicum sp. nov. (ex-type AS3.15900T = LN5H1-4), P. hepuense sp. nov. (ex-type AS3.16039T = TT2-4X3, AS3.16040 = TT2-6X3) and P. jiaozhouwanicum sp. nov. (ex-type AS3.16038T = 0801H2-2, AS3.16207 = ZZ2-9-3). In morphology, P. donggangicum is unique in showing light yellow sclerotia and mycelium, sparse sporulation, restricted growth at 37 °C, irregular conidiophores, intercalary phialides and metulae, and pyriform to subspherical conidia. P. hepuense is distinguished by the fast growth on CYA and YES and slow growth on MEA at 25 °C, weak or absence of growth at 37 °C, biverticillate and monoverticillate penicilli, and ellipsoidal conidia. P. jiaozhouwanicum is characterized by abundant grayish-green conidia en masse and moderate growth at 37 °C, the appressed biverticillate penicilli and fusiform, smooth-walled conidia. These three novelties were further confirmed by the phylogenetic analyses based on either the combined BenA-CaM-Rpb2 or the individual BenA, CaM, Rpb2 and internal transcribed spacer (ITS) sequences.
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Affiliation(s)
- Ke-Xin Xu
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Xia-Nan Shan
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yongming Ruan
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - JianXin Deng
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Calabon MS, Hyde KD, Jones EBG, Luo ZL, Dong W, Hurdeal VG, Gentekaki E, Rossi W, Leonardi M, Thiyagaraja V, Lestari AS, Shen HW, Bao DF, Boonyuen N, Zeng M. Freshwater fungal numbers. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00503-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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241
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Rokas A. Evolution of the human pathogenic lifestyle in fungi. Nat Microbiol 2022; 7:607-619. [PMID: 35508719 PMCID: PMC9097544 DOI: 10.1038/s41564-022-01112-0] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/25/2022] [Indexed: 02/07/2023]
Abstract
Fungal pathogens cause more than a billion human infections every year, resulting in more than 1.6 million deaths annually. Understanding the natural history and evolutionary ecology of fungi is helping us understand how disease-relevant traits have repeatedly evolved. Different types and mechanisms of genetic variation have contributed to the evolution of fungal pathogenicity and specific genetic differences distinguish pathogens from non-pathogens. Insights into the traits, genetic elements, and genetic and ecological mechanisms that contribute to the evolution of fungal pathogenicity are crucial for developing strategies to both predict emergence of fungal pathogens and develop drugs to combat them.
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Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
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242
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Kumar V, Joseph S, Sharma YP, Nayaka S. An annotated catalogue of the lichenicolous fungi of Jammu and Kashmir and Ladakh, India with new records and identification key. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2022. [DOI: 10.1016/j.japb.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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243
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Phukhamsakda C, Nilsson RH, Bhunjun CS, de Farias ARG, Sun YR, Wijesinghe SN, Raza M, Bao DF, Lu L, Tibpromma S, Dong W, Tennakoon DS, Tian XG, Xiong YR, Karunarathna SC, Cai L, Luo ZL, Wang Y, Manawasinghe IS, Camporesi E, Kirk PM, Promputtha I, Kuo CH, Su HY, Doilom M, Li Y, Fu YP, Hyde KD. The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00502-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractThe global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora, Bambusicola, Beltrania, Capronia, Distoseptispora, Endocalyx, Neocatenulostroma, Neodeightonia, Paraconiothyrium, Peroneutypa, Phaeoacremonium and Vanakripa. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.
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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: 11] [Impact Index Per Article: 3.7] [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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Munger IA, Baugh M, Henrie JR, Hollinger J, Crepeau R, Leavitt SD. Integrative Biodiversity Inventories: Characterizing Lichen-Forming Fungal Diversity in Glen Canyon National Recreation Area Using DNA Barcoding and Vouchered Specimens. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Isaac A. Munger
- Department of Biology, Brigham Young University, Provo, UT 84602
| | - Mikele Baugh
- Department of Biology, Brigham Young University, Provo, UT 84602
| | - Jacob R. Henrie
- Department of Biology, Brigham Young University, Provo, UT 84602
| | - Jason Hollinger
- Herbarium, Department of Biology, Western Carolina University, Cullowhee, NC 28723
| | - Robin Crepeau
- Department of Biology, Brigham Young University, Provo, UT 84602
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246
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Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data. mBio 2022; 13:e0244421. [PMID: 35404122 PMCID: PMC9040722 DOI: 10.1128/mbio.02444-21] [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] [Indexed: 11/20/2022] Open
Abstract
Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes.
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247
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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: 2.3] [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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Stallman JK, Robinson K. Importance of Seasonal Variation in Hawaiian Mushroom (Agaricomycetes) Basidiomata Production for Biodiversity Discovery and Conservation. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:869689. [PMID: 37746163 PMCID: PMC10512390 DOI: 10.3389/ffunb.2022.869689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/09/2022] [Indexed: 09/26/2023]
Abstract
The Hawaiian Islands have a relatively well-known funga for a tropical location, yet there are over 400 species of mushrooms (Agaricomycetes) in the archipelago that remain to be documented. Importantly, the International Union for Conservation of Nature (IUCN) recently evaluated six mushrooms endemic to the islands as threatened with extinction. To improve detection of mushrooms for biodiversity discovery and better monitor threatened species in the archipelago-where many localities lack strong annual precipitation patterns associated with an obvious season for increased mushroom basidiomata production-we examined the phenology of Hawaiian mushrooms. Monthly richness was determined from a literature review and abundance from online data repositories. Phenological patterns were separately explored for native species and differing elevation and annual precipitation categories. Despite relatively consistent monthly temperatures and areas with regular monthly rainfall, we found Hawaiian mushrooms generally exhibit uneven temporal patterns in basidiomata production: richness and abundance are generally highest in January and lowest from February to April, then usually increase from May to July and remain at elevated levels through December. This pattern does not occur when considering native species richness only, nor when examining abundance data stratified by elevation and annual rainfall categories. Increased monthly basidiomata abundance in low elevation (<1,000 m), dry (<1,000 mm rainfall/year) locations on O'ahu and low, mesic (1,000-2,500 mm rainfall/year) locations on O'ahu and Kaua'i are positively correlated with increased monthly rainfall. Phenology of macrofungal sporocarp production should potentially be included in species threat assessments by the IUCN to increase detection via traditional surveying methods.
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Affiliation(s)
- Jeffery K. Stallman
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Kyra Robinson
- Department of Biology, University of Hawaii at Hilo, Hilo, HI, United States
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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: 9] [Impact Index Per Article: 3.0] [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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