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We present a workflow for efficient barcoding of myxomycete fructifications, which (i) requires less than 1000 spores, (ii) allows to collect spores with only a needle, (iii) works without any commercial kits, and (iv) is optimized for the use of 96-well PCR plates throughout the process. Specimens of 291 dark-spored nivicolous myxomycetes and 121 bright-spored members of the Trichiaceae were sequenced for the barcode marker 18S rDNA (SSU) with a low rate of failure and no detectable cross-contamination. Crude DNA extracts can be stored for further analyses: the elongation factor 1 alpha gene (EF1A), a single-copy marker, was successfully amplified after four weeks of storage.As such our procedure will allow a time- and cost-efficient barcoding of large series of specimens.

Two species of nivicolous myxomycetes, Lamproderma pseudomaculatum and Lamproderma aff. pulchellum, previously considered as strictly montane, are reported from the lowlands (116–192 m a.s.l.) of the eastern Ukraine during three spring seasons. Lowland collections of L. aff. pulchellum show comparatively low genetic similarity with specimens of this species collected at high elevations and may represent a new taxon. Autumn frosts, which occurred before the formation of a stable snow cover, as well as the limited number of days with snow cover exceeding 30 cm, did not prevent the abundant fruiting of these myxomycetes.

Within the myxomycetes, phylogenetic research is still at a relatively early stage, and available phylogenies are often based on only a single or a few marker genes. According to the available data, the “true” myxomycetes (exosporous, myxogastric) form a monophyletic clade within the phylum Eumycetozoa with two basal subclades, a dark-spored (treated as the Columellomycetidae) and a bright-spored (the subclass Lucisporomycetidae). Within the first subclade the main evolutionary branches are recognized as the orders Echinosteliales, Echinosteliopsidales, Clastodermatales, Meridermatales, Stemonitidales, and Physarales; for the bright-spored subclade, these are the orders Cribrariales, Reticulariales, Liceales, and Trichiales. In the light of molecular data the traditional criteria used in myxomycete taxonomy have to be reevaluated. The morphology of capillitia and peridia, and especially how these two structures are connected to each other in a particular taxon, seems to be highly informative, whereas their presence or absence is not. Similarly, single versus compound fruiting bodies, a character often used to delimit genera, seems to deserve a lower weight, as these structures have evolved several times in parallel. Many, especially species rich, genera seem not to represent monophyletic units, and further research will most likely change their delimitation.

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., Nalin N. Wijayawardene thanks Mushroom Research Foundation and National Science Foundation of China (No. NSFC 31950410558) for financially supporting this project. Kevin D. Hyde acknowledges the Foreign Experts Bureau of Yunnan Province, Foreign Talents Program (2018; grant no. YNZ2018002), Thailand Research grants entitled Biodiversity, phylogeny and role of fungal endophytes on above parts of Rhizophora apiculata and Nypa fruticans (grant no: RSA5980068), the future of specialist fungi in a changing climate: baseline data for generalist and specialist fungi associated with ants, Rhododendron species and Dracaena species (grant no: DBG6080013), Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion (grant no: RDG6130001). H.T. Lumbsch thanks support by the Grainger Bioinformatics Center. E. Malosso is grateful to CAPES for financial support (grant no. 88881.062172/2014-01). B.T. Goto, G.A. Silva and K. Jobim, L.C. Maia acknowledges CNPq (Brazilian Scientific Council, grants no. 465.420/2014-1, 307.129/2015-2 and 408011/2016-5) and CAPES for support. The study was partially supported by the National Science Centre, Poland, under Grants No. 2015/17/D/NZ8/00778 and 2017/25/B/NZ8/00473 to Julia Pawłowska. The research of Martin Kukwa received support from the National Science Centre (NCN) in Poland (project no 2015/17/B/NZ8/02441). Alan J.L. Phillips acknowledges the support from UID/MULTI/04046/2019 Research Unit grant from FCT, Portugal to BioISI. H. Zhang is financially supported by the National Natural Science Foundation of China (Project ID: NSF 31500017). S. Boonmee would like to thank the Thailand Research Fund (Project No. TRG6180001). Dong-Qin Dai and Li-Zhou Tang would like to thank the National Natural Science Foundation of China (No. NSFC 31760013, NSFC 31260087, NSFC 31460561), the Scientific Research Foundation of Yunnan Provincial Department of Education (2017ZZX186) and the Thousand Talents Plan, Youth Project of Yunnan Provinces for support. R. Phookamsak, M. Doilom, D. N. Wanasinghe, S.C. Karunarathna and J.C. Xu express sincere appreciations to Key Research Program of Frontier Sciences of the Chinese Academy of Sciences (grant no. QYZDY-SSW-SMC014) for research financial support. R. Phookamsak thanks the Yunnan Provincial Department of Human Resources and Social Security (grant no. Y836181261), Chiang Mai University and National Science Foundation of China (NSFC) project code 31850410489 for research financial support. S.C. Kaunarathna thanks CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (No. 2018PC0006) and the National Science Foundation of China (NSFC) for funding this work under the project code 31851110759. S. Tibpromma would like to thank the International Postdoctoral Exchange Fellowship Program (number Y9180822S1), CAS President’s International Fellowship Initiative (PIFI) (number 2020PC0009), China Postdoctoral Science Foundation and the Yunnan Human Resources, and Social Security Department Foundation for funding her postdoctoral research. Yuri S. Tokarev, Elena S. Nassonova and Irma V. Issi are indebtful to Yuliya Y. Sokolova (Institute of Cytology RAS, St. Petersbug, Russia) and Anastasia V. Simakova (Tomsk State University, Tomsk, Russia) for kind permission of reproduction of electron microscopy images of Metchnikovella incurvata and Crepidulospora beklemishevi, respectively. Yuri S. Tokarev and Irma V. Issi thank Russian Foundation of Basic Research, grant number 17-04-00871 (taxonomy of Rozellomycota). Elena S. Nassonova thank Russian Foundation of Basic Research, grant number 18-04-01359 (early evolution of Microsporidia, phylogeny of Metchnikovellida). Adam Flakus and Pamela Rodriguez-Flakus are greatly indebted to all staff of the Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz and the SERNAP (http://sernap.gob.bo), for their generous cooperation providing permits, assistance and facilities support for scientific studies. The research of AF and PRF were financially supported by the National Science Centre (NCN) in Poland (DEC-2013/11/D/NZ8/03274). Adam Flakus and Pamela Rodriguez-Flakus received additional support under statutory funds from the W. Szafer Institute of Botany, Polish Academy of Sciences, Krakow, Poland. The authors would like to thank Yunnan Innovation Platform for Development and Utilization of Symbiotic Fungi Resources for finance support. Li-Fang Zhang would like to thank grant-in-aid from Science and Technology Department of Yunnan Province (2018FD080) for finance support. Chun-Ying Deng thanks the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (2019HJ2096001006). Yingqian Kang would like to thank Guizhou Scientific Plan Project [(2019) 2873]; Excellent Youth Talent Training Project of Guizhou Province [(2017) 5639]; Guiyang Science and Technology Project [(2017) No. 5-19]; Talent Base Project of Guizhou Province, China [FCJD2018-22]; Research Fund of Education Bureau of Guizhou Province, China [(2018) 481]. D. N. Wanasinghe would like to thank the CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (number 2019PC0008), the National Science Foundation of China and the Chinese Academy of Sciences for financial support under the following grants: 41761144055, 41771063 and Y4ZK111B01. Yuri K. Novozhilov and Oleg N. Shchepin acknowledge support from the Russian Foundation of Basic Research, project 18-04-01232 А. Ivana Kušan, Neven Matočec, Armin Mešić and Zdenko Tkalčec are grateful to Croatian Science Foundation for their financial support under the project grant HRZZ-IP-2018-01-1736 (ForFungiDNA). K. Tanaka would like to thank the Japan Society for the Promotion of Science (JSPS 19K06802)

Background and aims – Recent studies showed the position of two slime mould species with microscopic sporocarps, Echinosteliopsis oligospora and Echinostelium bisporum, within the class Myxomycetes. These minute species are seldom seen in studies based on detection of sporocarps and can easily be confused with protosteloid amoebozoans.Methods – We searched all published ePCR data sets that targeted myxomycete 18S rDNA for the presence of environmental sequences similar to E. oligospora and Echinosteliales in traditional circumscription, and performed phylogenetic analyses that included short environmental sequences and full-length 18S rDNA sequences representing all the major groups of myxomycetes.Key results – We report 19 unique sequences which are closely related to E. bisporum or E. oligospora based on sequence similarity (73.1–95.2% similarity) and which form well-supported monophyletic clades with these species in phylogenetic analyses. They may represent new species that are not yet described. Our phylogeny based on full-length 18S rDNA sequences further confirms the position of E. bisporum and E. oligospora within myxomycetes and the paraphyly of the order Echinosteliales in its traditional circumscription.Conclusions – Our results show that ePCR-based studies can reveal myxomycete taxa that often escape detection by traditional approaches, including potentially new species, and thus provide valuable new data on diversity and ecology of myxomycetes. As such, strategies for studying myxomycetes biodiversity should be revised, focusing also on molecular detection techniques in addition to the sporocarp-based ones.

The genus Siphoptychium is resurrected on the basis of comparative morphology and phylogeny of partial nuc 18S rDNA (18S) and translation elongation factor 1-alpha (EF1A) nucleotide sequences. The genus is characterized by the firm upper surface of the pseudoaethalium, accreted but easily separable sporothecae, a tubular or fibrous columella, and spores with a reticulate ornamentation consisting of 7-9 meshes across the diameter. In addition to the currently known single species S. casparyi (= Tubifera casparyi), two new members of Siphoptychium are described: S. violaceum from coniferous forests of Europe, east Asia, and southeast Asia, and S. reticulatum from temperate and subarctic regions of North America and alpine regions of Europe. A second genus, Thecotubifera, is described to accommodate Tubifera dictyoderma. The fruiting body of this species is transitional between a pseudoaethalium and a true aethalium. It is covered by a contiguous membranous cortex formed by the fused tips of the sporothecae, a feature typical for aethalia. However, the inner portions of sporothecae remain discernible, a feature more typical for pseudoaethalia. Columellae of Th. dictyoderma are formed by perforated plates, and the spores have a reticulate ornamentation consisting of 2-5 meshes across the diameter. For Th. dictyoderma, we could confirm records only for tropical regions and Japan, whereas all studied European specimens, including those mentioned in current monographs, represent species of Siphoptychium.

Three new myxomycete species, Tubifera glareata, T. tomentosa and T. vanderheuliae, are described on the basis of morphological investigations and the partial 18S rDNA barcoding. Tubifera vanderheuliae, collected in Tasmania and New South Wales, is characterized by small, bouquet-shaped pseudoaethalia, cylindrical sporothecae somewhat extended at the top, and the largest spores known thus far within the genus (7.5–10.5 μm). Tubifera glareata, found thus far only in Tasmania, is somewhat similar to T. applanata found in the Holarctic region, but differs from the latter by the larger spores, absence of ring-like ornamentation on the peridium, and the smaller subspherical pseudoaethalia. Tubifera tomentosa, also collected in Tasmania, differs from the related species T. dudkae by the conspicuous amorphous felt-like cover on the surface of the pseudoaethalia.

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.

The genus

A new species of myxomycete, Perichaena longipes, is described from 56 sporocarp specimens that appeared in moist chamber cultures prepared with samples of decaying plant materials collected in Panama, Costa Rica and Brazil. This new species is distinguished from the morphologically similar species P. pedata on the basis of the much longer stipe, lighter peridium and the unique ornamentation of the capillitium. The nuc 18S ribosomal DNA sequences obtained from four specimens of P. longipes support the distinction of this new taxon and its separation from P. pedata. Furthermore, maximum likelihood phylogeny supports earlier evidence that species currently within the genus Perichaena do not form a monophyletic clade. Instead they appear to form three separate branches within the bright-spored clade. The first clade includes P. longipes together with several species of Trichia and Metatrichia, the second includes P. pedata and P. chrysosperma, and the third clade is composed of P. corticalis, P. depressa and P. luteola.

Based on a morphological investigation of a series of specimens collected in New South Wales and Tasmania and a phylogeny constructed with partial 18S ribosomal RNA gene sequences, we describe a new species Alwisia lloydiae; the fourth species within the recently revalidated genus Alwisia. This new species is characterized by short ovate sporothecae with mostly free stalks, morphologically resembling the recently described A. morula. However, the new species possesses a tubular capillitium that suggests an affinity with A. bombarda. The capillitium of the new species is ornamented with globular warts, and this feature separates it from all other members of the genus.

W e studied the capillitial structures produced in Alwisia bombarda (Reticulariaceae, Myxomycetes) by light and electron microscopy. This species develops tubular threads inside of clustered but still separate sporocarps with intact walls forming a cup. These threads have been considered to be a pseudocapillitium for a long time, but they do not represent remains of confluent peridia and thus do not correspond to the classical definition of a pseudocapillitium. Instead, they should be considered as a true capillitium. The structure of the capillitium in A. bombarda is very similar to that found in the genera Dianema and Lycogala, thus providing a new argument for a close relationship between the Reticulariaceae and Dianemataceae and also for considering the tubular threads of Lycogala as representing a true capillitium.

Based on morphological investigations and a phylogeny constructed with partial sequences of the SSU rDNA gene, we revalidate the genus Alwisia and propose the combination Alwisia bombarda Berk. & Broome to be used against Tubifera bombarda (Berk. & Broome) G.W. Martin. Two new species, Alwisia morula and A. repens, are described based on material collected respectively in Costa Rica and Australia. Both new species lack a capillitium and possess individually stalked subspherical sporothecae. Alwisia repens differs from A. morula by its procumbent stalks and iridescent peridium. A comparison of 83 sequences of species in the genera Lycogala, Reticularia and Tubifera with a recent two-gene phylogeny of the bright-spored myxomycetes resulted in a similar topology of both Bayesian and maximum likelihood trees and placed A. bombarda, A. morula and A. repens in one well delimited clade within Reticulariaceae. Universidad de Costa Rica/[VI-731-B2-224]/UCR/Costa Rica UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ingeniería::Instituto Investigaciones en Ingeniería (INII)

The traditional classification of the Myxomycetes (Myxogastrea) into five orders (Echinosteliales, Liceales, Trichiales, Stemonitidales and Physarales), used in all monographs published since 1945, does not properly reflect evolutionary relationships within the group. Reviewing all published phylogenies for myxomycete subgroups together with a 18S rDNA phylogeny of the entire group serving as an illustration, we suggest a revised hierarchical classification, in which taxa of higher ranks are formally named according to the International Code of Nomenclature for algae, fungi and plants. In addition, informal zoological names are provided. The exosporous genus Ceratiomyxa, together with some protosteloid amoebae, constitute the class Ceratiomyxomycetes. The class Myxomycetes is divided into a bright- and a dark-spored clade, now formally named as subclasses Lucisporomycetidae and Columellomycetidae, respectively. For bright-spored myxomycetes, four orders are proposed: Cribrariales (considered as a basal group), Reticulariales, a narrowly circumscribed Liceales and Trichiales. The dark-spored myxomycetes include five orders: Echinosteliales (considered as a basal group), Clastodermatales, Meridermatales, a more narrowly circumscribed Stemonitidales and Physarales (including as well most of the traditional Stemonitidales with durable peridia). Molecular data provide evidence that conspicuous morphological characters such as solitary versus compound fructifications or presence versus absence of a stalk are overestimated. Details of the capillitium and peridium, and especially how these structures are connected to each other, seem to reflect evolutionary relationships much better than many characters which have been used in the past.

Within the myxomycetes, phylogenetic research is still at a relatively early stage; available phylogenies are often based on only a single or a few marker genes. In this chapter, we review the molecular data currently available on the position of myxomycetes in relation to other eukaryotic organisms, and compare these with existing classifications of the group. If the genus Ceratiomyxa is considered separately to all other myxomycetes, the latter are monophyletic. Unambiguously supported by all molecular markers is a split into two basal clades, a dark-spored clade and a bright-spored clade, which is largely in accordance with the traditional classification based on five orders. However, most of these orders are not supported as monophyletic groups, although a new delimitation is difficult due to the low proportion of species hitherto investigated with molecular markers. In the light of molecular data, the traditional criteria used in myxomycete taxonomy have to be reevaluated. The morphology of capillitia and peridia, and especially how these two structures are connected to each other, seems to be highly informative, whereas their presence or absence is not. Similarly, single versus compound fruiting bodies, a character often used to delimit genera, seems to deserve a lower weight, as these structures have evolved several times in parallel. Further research employing molecular markers will most likely lead to a revised hierarchical classification of the myxomycetes.

Myxomycetes, or plasmodial slime molds, are a group of lower eukaryotes that grow and feed at the motile phase of the life cycle, named plasmodium, and produce complex fruiting bodies at the reproductive phase. Most of them live on land, mainly in forest ecosystems (Stephenson, 1988). Phytocenotic connections of myxomycetes in the forest‐steppe zone of Ukraine have not been previously studied. It remains unknown to what extent the foreststeppe biota of these organisms depends on vegetation and in which of its parameters (species richness, the composition of dominant species, the proportion of unique species, etc.) this dependence is manifested. Specific features of the myxomycete biota in zonal phytocenoses and phytocenoses that do not belong to the zonal vegetation of this region are also unknown.