Outline of Fungi and fungus-like taxa – 2021

This paper provides an updated classification of the Kingdom Fungi (including fossil fungi) and fungus-like taxa. Five-hundred and twenty-three (535) notes are provided for newly introduced taxa and for changes that have been made since the previous outline. In the discussion, the latest taxonomic changes in Basidiomycota are provided and the classification of Mycosphaerellales are broadly discussed. Genera listed in Mycosphaerellaceae have been confirmed by DNA sequence analyses, while doubtful genera (DNA sequences being unavailable but traditionally accommodated in Mycosphaerellaceae) are listed in the discussion. Problematic genera in Glomeromycota are also discussed based on phylogenetic results.National Natural Science Foundation of China (NSFC) NSFC 31950410558 NSFC 31760013 32100011Department of Science and Technology of Yunnan Province 2018FB050State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University FAMP201906KScience and Technology Department of Guizhou Province QKHRCPT[2017] 5101High-Level Talent Recruitment Plan of Yunnan Province ("Young Talents" Program)Chiang Mai UniversityCroatian Science Foundation HRZZ-IP-2018-01-1736 HRZZ-2018-09-7081LOEWE initiative of the government of HessenDistinguished Scientist Fellowship (DSFP), King Saud University, Kingdom of Saudi ArabiaCAS President's International Fellowship Initiative (PIFI) 2020PB0115 2020PC0009 2018PC0006National Science Centre, Poland 2017/25/B/NZ8/00473International Postdoctoral Exchange Fellowship Program Y9180822S1China Postdoctoral Science FoundationYunnan Human Resources, and Social Security Department FoundationNational Natural Science Foundation of China (NSFC) 31750110478China Postdoctoral Science Foundation 2021M693361Portuguese Foundation for Science and TechnologyEuropean Commission UIDB/04046/2020 UIDP/04046/2020High-Level Talent Recruitment Plan of Yunnan Province ("High-End Foreign Experts" Program

Current Insight into Culture-Dependent and Culture- Independent Methods in Discovering Ascomycetous Taxa

This research was funded by the National Natural Science Foundation of China (No. NSFC 31950410558, NSFC 31760013), the State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medicial University (No. FAMP201906K); Science and Technology Department of Guizhou Province (QKHRCPT [2017]5101) and High-Level Talent Recruitment Plan of Yunnan Provinces ("Young Talents" Program and "High-End Foreign Experts" Program).Nalin N. Wijayawardene and Dong-Qin Dai gratefully acknowledge Paul M. Kirk, Sandhya Jayasekara, Shalini Rajakaruna, D. Siril A. Wijesundara, Steve L. Stephenson, R.P. Prabat K. Jayasinghe, Samantha C. Karunarathne, Faruk Selcuk, Makbule Erdogdu and Kevin D. Hyde for their suggestions and support.Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual-asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.National Natural Science Foundation of China (NSFC) NSFC 31950410558- NSFC 31760013State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medicial University FAMP201906KScience and Technology Department of Guizhou Province QKHRCPT [2017]5101High-Level Talent Recruitment Plan of Yunnan Province

A dynamic portal for a community-driven, continuously updated classification of Fungi and fungus-like organisms: outlineoffungi.org

The website http://outlineoffungi.org, is launched to provide a continuous up-to-date classification of the kingdom Fungi (including fossil fungi) and fungus-like taxa. This is based on recent publications and on the outline of fungi and fungus-like taxa published recently (Mycosphere 11, 1060-1456, Doi: 10.5943/mycosphere/11/1/8). The website is continuously updated according to latest classification schemes, and will present an important platform for researchers, industries, government officials and other users. Users can provide input about missing genera, new genera, and new data. They will also have the opportunity to express their opinions on classifications with notes published in the 'Notes' section of the webpage following review and editing by the curators and independent experts. The website will provide a system to stay abreast of the continuous changes in fungal classification and provide a general consensus on the systematics of fungi

Comparing Floristic Diversity between a Silviculturally Managed Arboretum and a Forest Reserve in Dambulla, Sri Lanka

Repeated slash and burn cultivation creates wasteland with thorny shrubs, which then takes a long time to become secondary forests through serial stages of succession. Assisted natural regeneration through silvicultural management is a useful restoration method to accelerate succession. This survey evaluates the effectiveness of a simple silvicultural method for the rehabilitation of degraded lands to productive forest, thereby increasing floristic wealth. Field-based comparative analyses of floristic composition were carried out at a silviculturally managed forest (Popham Arboretum) and a primary forest (Kaludiyapokuna Forest Reserve) which is located in Dambulla in Sri Lanka. Floristic analysis was used to examine the effectiveness of silvicultural techniques for successful restoration of degraded forest in the dry zone. Nine 20 m × 20 m plots in each forest were enumerated and the vegetation ≥ 10 cm girth at breast height was quantitatively analyzed. Cluster analysis resulted in five distinguishable clusters (two from Popham Arboretum and three from Kaludiyapokuna Forest Reserve). Similarity indices were generated to compare the plots within and between sites. Floristic similarity was higher in forest reserve plots compared to arboretum plots. A total of 72 plant species belonging to 60 genera and 26 families were recorded from the study sites. Of the recorded species, Grewia damine and Syzygium cumini (Importance Value Index, IVI = 24 and 23 respectively) were the ecologically co-dominant taxa at the Popham Arboretum. In contrast, Mischodon zeylanicus (IVI = 31), Schleichera oleosa (IVI = 25) and Diospyros ebenum (IVI = 21) were the abundant taxa in the forest reserve

Taxonomic and phylogenetic characterisations of six species of Pleosporales (in Didymosphaeriaceae, Roussoellaceae and Nigrogranaceae) from China

Pleosporales comprise a diverse group of fungi with a global distribution and significant ecological importance. A survey on Pleosporales (in Didymosphaeriaceae, Roussoellaceae and Nigrogranaceae) in Guizhou Province, China, was conducted. Specimens were identified, based on morphological characteristics and phylogenetic analyses using a dataset composed of ITS, LSU, SSU, tef1 and rpb2 loci. Maximum Likelihood (ML) and Bayesian analyses were performed. As a result, three new species (Neokalmusia karka, Nigrograna schinifolium and N. trachycarpus) have been discovered, along with two new records for China (Roussoella neopustulans and R. doimaesalongensis) and a known species (Roussoella pseudohysterioides). Morphologically similar species and phylogenetically close taxa are compared and discussed. This study provides detailed information and descriptions of all newly-identified taxa

Corrigendum: Hu H et al. (2023) Taxonomic and phylogenetic characterisations of six species of Pleosporales (in Didymosphaeriaceae, Roussoellaceae and Nigrogranaceae) from China. MycoKeys 100: 123–151. https://doi.org/10.3897/mycokeys.100.109423

Four new species, Xynobius azonius sp. nov., X. brevifemora sp. nov., X. duoferus sp. nov., and X. stipitoides sp. nov., are described and illustrated, and one species X. geniculatus (Thomson, 1895) is newly reported from South Korea. Xynobius geniculatus (Thomson, 1895) is redescribed and illustrated, and a new combination, Xynobius (Stigmatopoea) cubitalis (Fischer, 1959), comb. nov. is suggested. An identification key to the Xynobius species known from South Korea is provided

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi

Outline of fungi and fungus-like taxa

This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi.Fil: Wijayawardene, N. N.. Qujing Normal University; ChinaFil: Hyde, K. D.. Mae Fah Luang University; TailandiaFil: Al-Ani, L. K. T.. University of Baghdad; IraqFil: Tedersoo, L.. University of Tartu; EstoniaFil: Haelewaters, D.. University of South Bohemia; República Checa. Purdue University; Estados Unidos. Universidad Autónoma de Chiriquí; PanamáFil: Becerra, Alejandra Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Schnittler, M.. Ernst Moritz Arndt University Greifswald; AlemaniaFil: Shchepin, O. N.. The Komarov Botanical Institute of the Russian Academy of Sciences; RusiaFil: Novozhilov, Y. K.. The Komarov Botanical Institute of the Russian Academy of Sciences; RusiaFil: Silva-Filho, A.G. S.. Universidade Federal do Rio Grande do Norte; BrasilFil: Gentekaki, E.. Mae Fah Luang University; TailandiaFil: Liu, P.. Jilin Agricultural University; ChinaFil: Cavender, J. C.. Ohio University; Estados UnidosFil: Kang, Y.. Guizhou Medical University; ChinaFil: Mohammad, S.. Iranian Research Organization for Science and Technology; IránFil: Zhang, L. F.. Qujing Normal University; ChinaFil: Xu, R. F.. Qujing Normal University; ChinaFil: Li, Y. M.. Qujing Normal University; ChinaFil: Dayarathne, M. C.. Guizhou University; ChinaFil: Ekanayaka, A. H.. Mae Fah Luang University; TailandiaFil: Wen, T. C.. Guizhou University; ChinaFil: Deng, C. Y.. Guizhou Academy of Science; ChinaFil: Pereira, O. L.. Universidade Federal de Viçosa; BrasilFil: Navathe, S.. Agharkar Research Institute; IndiaFil: Hawksworth, D. L.. The Natural History Museum; Reino UnidoFil: Fan, X. L.. Beijing Forestry University; ChinaFil: Dissanayake, L. S.. Guizhou University; ChinaFil: Kuhnert, E.. Leibniz University Hannover; AlemaniaFil: Grossart, H. P.. Leibnitz Institute of Freshwater Ecology and Inland Fisheries; AlemaniaFil: Thines, M.. Senckenberg Biodiversity and Climate Research Centre; Alemani

Potential Fungi Isolated From Anti-biodegradable Chinese Medicine Residue to Degrade Lignocellulose

Traditional Chinese medicine is one of the ancient medicines which is popular in Asian countries, among which the residue produced by the use of anti-biodegradables is endless, and causes significant adverse impacts on the environment. However, the high acidity of anti-biodegradable residues and some special biological activities make it difficult for microorganisms to survive, resulting in a very low degradation rate of lignocellulose in naturally stacked residues, which directly impedes the degradation of residues. We aimed to identify the fungal strains that efficiently biodegrade anti-biodegradable residue and see the possibility to improve the biodegradation of it and other agricultural wastes by co-cultivating these fungi. We isolated 302 fungal strains from anti-biodegradable residue to test hydrolysis ability. Finally, we found Coniochaeta sp., Fomitopsis sp., Nemania sp., Talaromyces sp., Phaeophlebiopsis sp. which inhabit the anti-biodegradable residues are capable of producing higher concentrations of extracellular enzymes. Synergistic fungal combinations (viz., Fomitopsis sp. + Phaeophlebiopsis sp.; Talaromyces sp. + Coniochaeta sp. + Fomitopsis sp.; Talaromyces sp. + Fomitopsis sp. + Piloderma sp. and Talaromyces sp. + Nemania sp. + Piloderma sp.) have better overall degradation effect on lignocellulose. Therefore, these fungi and their combinations have strong potential to be further developed for bioremediation and biological enzyme industrial production

Naming and outline of Dothideomycetes-2014 including proposals for the protection or suppression of generic names

Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in Dothideomycetes (belonging to 23 orders and 110 families), including pleomorphic and nonpleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes. A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data