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In production forests, a common silvicultural objective is enhancing tree growth rates. The growth rate influences both mechanical and biochemical properties of wood, which may have an impact on dead wood inhabiting (i.e. saproxylic) species. In this study, we tested for the first time whether tree growth rates affect dead-wood associated assemblages in general and the occurrence of red-listed species in particular. We sampled saproxylic beetles (eclector traps) and fungi (DNA metabarcoding of wood samples) in dead trunks of Norway spruce (Picea abies), which had different growth rates within the same hemiboreal forests in Sweden. A high proportion of fungi showed a positive association to increasing tree growth. This resulted in higher fungal richness in fast-grown trees both at the trunk scale and across multiple studied trunks. Such patterns were not observed for saproxylic beetles. However, a set of species (both beetles and fungi) preferred slow-grown wood. Moreover, the total number of red-listed species was highest in slow-grown trunks. We conclude that dead wood from slow-grown trees hosts relatively fewer saproxylic species, but a part of these may be vulnerable to production forestry. It implies that slow-grown trees should be a target in nature conservation. However, where slow-grown trees are absent, for instance in forests managed for a high biomass production, increasing the volumes of dead wood from fast-grown trees may support many species. Supplementary Information The online version contains supplementary material available at 10.1007/s00442-021-05061-z.

Amongst the complicated group of Peziza with blue-violet-purplish hymenial surface, P. petersii, P. proteana f. proteana and f. sparassoides were studied using both morphological and molecular approaches (analysis of the nrITS and RPB2 sequences). The nrITS sequences were successfully obtained from the holotypes of Aleuria proteana, P. pseudoviolacea and Underwoodia campbellii. The epitype collection of P. petersii was designated, and its nrITS and RPB2 regions were sequenced. Our analyses showed that (i) P. proteana and P. petersii are a single species, and since P. petersii Berk. was published in 1875 and Aleuria proteana Boud. in 1899, the prioritary name is the former; (ii) P. proteana f. sparassoides (Boud.) Korf, the “cabbage-head fungus”, is a distinct evolutionary line and is here recognised at species level using the oldest available epithet that can be combined in Peziza, Underwoodia campbellii Sacc. Consequently, Peziza campbellii nov. comb. is introduced.

Three new species, closely related to Sphaerostilbella broomeana, are described from the USA and India. These species form septate conidia from simple conidiophores with individual branches terminating in a single phialide and chlamydospores. Teleomorphs, known for S. broomeana and S. appalachiensis, are characterised by hairy perithecia and fusiform, apiculate, and conspicuously warted ascospores. This combination of characters distinguishes the S. broomeana-group from other members of Sphaerostilbella that all form gliocladium-type anamorphs and mostly grow on basidiomata of Stereum spp. Like in other species of the genus, the majority of hosts of the species described in this paper belong to wood-inhabiting taxa of Russulales. Sphaerostilbella broomeana had been recorded from a few regions in Europe and exclusively on Heterobasidion annosum. Herein, it is reported also from H. parviporum in many other localities and on H. insulare s.l. at the foothills of the Himalayas. Its sister species, found in the same region in northern India on another member of Russulales (Dichostereum effuscatum), is described as S. himalayensis. The two species described from North America colonize polypores from various taxa. Whereas S. appalachiensis occurs in eastern USA, with H. irregulare among its hosts, S. toxica is so far known only from two locations in eastern Texas, growing on Gloeophyllum striatum (Polyporales). Despite their great similarity in morphology and ITS rDNA, TEF1 sequences clearly distinguish these two North-American species. Moreover, the two strains of S. toxica appeared metabolically distinct as their organic extracts strongly inhibited the growth of human pathogenic microbes grown in vitro. Phylogenetic analysis of rDNA sequences supports monophyly of the genus Sphaerostilbella and the included S. broomeana-group, established here.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN. Publisher’s Note A first version of this text was prepared by the first eight authors and the last one, given here. The other listed co-authors in the article PDF support the content, and their actual contributions varied from only support to additions that substantially improved the content. The full details of all co-authors, with their affiliations, are included in Supplementary Table 1 after p.175 of the article for reasons of clarity and space. Slavomír Adamčík Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23 Bratislava, Slovakia Teuvo Ahti Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland M. Catherine Aime Purdue University, 915 W. State St., West Lafayette, Indiana 47907, U.S.A. A. Martyn Ainsworth Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom László Albert Hungarian Mycological Society, 1087 Könyves Kálmán krt. 40, Budapest, Hungary Edgardo Albertó Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, Universidad Nacional de San Martin-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina Alberto Altés García Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Dmitry Ageev SIGNATEC Ltd., 630090, Novosibirsk, Akademgorodok (Novosibirsk Scientific Center), Inzhenernaya str., 22, Russia Reinhard Agerer Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 München, Germany Begona Aguirre-Hudson Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom Joe Ammirati University of Washington, Seattle, Washington 98195-1800, U.S.A. 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Moscoso, Apartado 21-9, Santo Domingo, Dominican Republic Vladimír Antonín Moravian Museum, Zeny trh 6, 659 37 Brno, Czech Republic Takayuki Aoki Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan André Aptroot ABL Herbarium, G.v.d.Veenstraat 107, 3762 XK Soest, The Netherlands Didier Argaud 40 rue du Justemont, 57290 Fameck, France Blanca Imelda Arguello Sosa Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Ciudad Victoria, Tamaulipas, Mexico Arne Aronsen Torødveien 54, 3135 Torød, Norway Ulf Arup Biological Museum, Lund University, Box 117, 221 00 Lund, Sweden Bita Asgari Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization, Tehran, Iran Boris Assyov Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Str., 1113 Sofia, Bulgaria Violeta Atienza Facultad de Ciencias Biológicas, Universitat de València, C/Dr Moliner 50, 46100, Burjasot, Valencia, Spain Ditte Bandini Panoramastr 47, 69257 Wiesenbach, Germany João Luís Baptista-Ferreira Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal Hans-Otto Baral Blaihofstr. 42, 72074 Tübingen, Germany Tim Baroni The State University of New York, 340 Bowers Hall, P.O. 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Bart Buyck Muséum National d’Histoire Naturelle, CP 39, ISYEB, UMR 7205 CNRS MNHN UPMC EPHE, 12 rue Buffon, 75005 Paris, France Ana Rosa Burgaz Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain Vicent Calatayud Fundación CEAM, c/ Charles R. Darwin, 14, Parque Tecnológico, 46980 Paterna, Valencia, Spain Philippe Callac INRA, MycSA, CS 20032, 33882 Villenave d’Ornon, France Emanuele Campo Associazione Micologica Bresadola, Via Alessandro Volta 46, 38123 Trento, Italy Massimo Candusso Via Ottone Primo 90, 17021, Alassio, Savona, Italy Brigitte Capoen Queffioec, rue de Saint Gonval, 22710 Penvenan, France Joaquim Carbó Roser, 60, 17257 Torroella de Montgrí, Girona, Spain Matteo Carbone Via Don Luigi Sturzo 173 16148 Genova, Italy Rafael F. Castañeda-Ruiz Instituto de Investigaciones Fundamentales en Agricultura, Tropical ‘Alejandro de Humboldt’, OSDE, Grupo Agrícola, Calle 1 Esq. 2, Santiago de Las Vegas, C. Habana 17200, Cuba Michael A. 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Zhurbenko Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia The following institutions are also supporting the present text (institutional support means that committees from the mentioned) Asociación Micológica Carlos Spegazzini (Argentina) Austrian Mycological Society (Austria) Croatian Mycological Society (Croatia) Committee of the Czech Scientific Society for Mycology (Czech Republic) The Netherlands Mycological Society (The Netherlands) Sociedad Española de Liquenología (Portugal/Spain) Iberian Mycological Society (which is under constitution, Portugal/Spain) Federación de Asociaciones Micológicas Andaluzas (FAMA) (Spain) Asociación Botánica y Micológica de Jaén (Spain) Asociación Micológica Hispalense Muscaria (Spain) Societat Micològica Valenciana (Spain)

This study focuses on the genus Encoelia and the subfamily Encoelioideae in the morphologically and ecologically diverse Helotiales. The 28S and 18S rDNA as well as tef1, rpb1 and rpb2 were sequenced for 70 species. Phylogenetic analyses revealed Encoelia and Encoelioideae to be highly polyphyletic, with species distributed among eight major lineages. Encoelia fascicularis and E. pruinosa belonged to Sclerotiniaceae and were combined in a new genus, Sclerencoelia. Rutstroemiaceae comprised E. tiliacea and Dencoeliopsis johnstonii, both accepted in Rutstroemia. The type of Encoelia, E. furfuracea, was closely related to species of Velutarina, Cenangiopsis and Crumenulopsis. These species together with members of Hemiphacidiaceae formed a clade conforming to the emended concept of Cenangiaceae, introduced here. Another resurrected family, Cordieritidaceae, comprised E. fimbriata, E. heteromera and species of Ameghiniella, Cordierites, Diplocarpa and Ionomidotis, characterised by inamyloid asci and a positive ionomidotic reaction. Encoelia glauca showed closest affinities with Chlorociboria species in Chlorociboriaceae. A new genus, Xeropilidium, with sporodochial and pycnidial synanamorphs, was described for the distinct encoelioid member of the Chaetomellaceae, previously known as E. fuckelii. Morphological and ecological synapomorphies were distinguished from convergent characters to delimit monophyletic taxa including encoelioid fungi. Incorporation of public sequences from various biological samples in ITS rDNA analyses allowed identification of sequenced organisms at species, genus, or family level and added information on the ecology of seversal taxa. Members of Cenangiaceae appeared to be widespread as endophytes. Inclusion of encoelioid genera in Chaetomellaceae and Sclerotiniaceae added xylicolous saprotrophs to these families.

In ecological and biodiversity research, fungal species are traditionally recorded using fruit body sampling, which underestimates mycelial presence of species. We hypothesized that fruit body based species lists are increasingly complete in larger sampling units where fruit bodies can be detected across multiple mycelial occurrences. We compared molecular records (detected with Illumina high-throughput sequencing) and records of fruit bodies of polypores in Estonian wetland pine forests. Of all molecularly detected polypores, 75% were present as conspecific fruit bodies within 30 m (including 24% on the same tree). This distance varied little among study sites. Despite lower costs, fruit body surveys yielded 60 polypore species, while sequencing only detected 13 species. Fruit body surveys of selected macrofungi can be thus efficient for biodiversity assessments. However, combining such surveys with high-throughput sequencing can add a broad description of the whole fungal assemblage even with limited samples (616 OTUs from 30 downed trunks in our study).

Fungi from the Ceratobasidiaceae family have important ecological roles as pathogens, saprotrophs, non-mycorrhizal endophytes, orchid mycorrhizal and ectomycorrhizal symbionts, but little is known about the distribution and evolution of these nutritional modes. All public ITS sequences of Ceratobasidiaceae were downloaded from databases, annotated with ecological and taxonomic metadata, and tested for the non-random phylogenetic distribution of nutritional modes. Phylogenetic analysis revealed six main clades within Ceratobasidiaceae and a poor correlation between molecular phylogeny and morphological–cytological characters traditionally used for taxonomy. Sequences derived from soil (representing putative saprotrophs) and orchid mycorrhiza clustered together, but remained distinct from pathogens. All nutritional modes were phylogenetically conserved in the Ceratobasidiaceae based on at least one index. Our analyses suggest that in general, autotrophic orchids form root symbiosis with available Ceratobasidiaceae isolates in soil. Ectomycorrhiza-forming capability has evolved twice within the Ceratobasidiaceae and it had a strong influence on the evolution of mycoheterotrophy and host specificity in certain orchid taxa.

Temperate species of Hypomyces and Cladobotryum that produce the red pigment aurofusarin are common on agaricoid and polyporoid basidiomata of species from five orders of Agaricomycetes. Several cause cobweb disease of commercially cultivated mushrooms resulting in serious losses. We sequenced rpb1, rpb2, tef1, and FG1093 regions in 90 wild strains and 30 strains from mushroom farms, isolated from Europe, North America, Africa, Asia, Australia, and New Zealand. Multigene analyses support the distinctness of five species but reveal Hypomyces rosellus to be paraphyletic, comprising several cryptic lineages. Hypomyces rosellus s. str. is characterised by wide dispersal and gene flow across Eurasia but does not occur in North America. Instead, the lineages from the West and the East Coast appear distinct, having given rise to species inhabiting the Southern Hemisphere. Our results reveal wide misuse of the name H. rosellus, especially for cobweb isolates. The majority of these belong to Hypomyces odoratus, including a weakly supported group of fungicide-resistant strains from Europe and North America sharing identical sequence data. New collections are presented for Cladobotryum rubrobrunnescens and Cladobotryum tenue as well as Cladobotryum multiseptatum and Hypomyces dactylarioides, all previously known only from their type material. The former species pair occurs in Europe and the latter in Australia and New Zealand. Separate lineages appear to be maintained by geographic isolation in North America and temperate Australasia but by host specialisation in the species occurring sympatrically in Europe and Asia. Both specialist and generalist host use strategies have evolved in the group. Although teleomorphs are known in most of the species and unnamed lineages, analyses of the five-gene regions suggest the prevalence of clonal reproduction in H. odoratus. This can be the reason for its success in mushroom farms, also facilitating the spread of fungicide resistance. While tef1 and rpb2 can be recommended for species delimitation, low variation, not exceeding 1 % in the whole ingroup, impeaches the use of ITS as a barcoding gene region in this group of fungi.

Two new species of hypogeous Pezizales in the Pyronemataceae are described from montane cloud forests in Mexico. Genea mexicana can be recognised by ITS sequence analysis and its distinct spore and seta dimensions; Geopora tolucana by ITS sequence analysis and its light brown hymenium, broadly ellipsoid ascospores and host preference. It belongs to the group of Geopora cooperi Harkn., which appears to be a rather heterogeneous assemblage, comprising a number of cryptic species. Our results indicate that the genus Geopora is non-monophyletic, occurring in two distinct phylogenetic clusters comprising species with either epigeous apothecial or hypogeous ptychothecial ascomata. Moreover, molecular divergence of Geopora is much higher than that of the neighbouring genera. Accordingly, we propose to reassign the cupulate apothecial Geopora species to the genus Sepultaria.

Species delimitation in the genus Geopora (Pyronemataceae) is complicated because of small number of differentiating characters, values of which tend to overlap among the species. Current classification relies mainly on size and shape of ascospores and fruit-bodies, position of the apothecia in the ground and length of excipular hairs. We measured ascospores in ca. 90 Geopora specimens. Sequences of internal transcribed spacer (ITS) rDNA gene were obtained to investigate phylogenetic relationships in the genus. Maximum parsimony (MP) and Bayesian analyses reveal that the well-supported clades detected often do not correspond to the species concepts based on morphological characters. Nine out of the ten lineages include specimens which were initially identified as belonging to different species. The dimensions of ascospores vary to great extent within the lineages. The size and shape of fruit-bodies, length of excipular hair and hymenium colour are mostly homogenous within each clade; however, these characters coincide to a great extent among the lineages and the latter can be assessed only from fresh fruit-bodies. Nuclear DNA content, and accordingly, ploidy level do not provide evidence for species distinction. Geopora arenicola, G. tenuis and G. sepulta were recognized as monophyletic species. Geopora foliacea and G. cervina could not be explicitly delimited and the G. cervina complex comprising three clades was introduced.

Summary Mycorrhizosphere microbes enhance functioning of the plant–soil interface, but little is known of their ecology. This study aims to characterize the ascomycete communities associated with ectomycorrhizas in two Tasmanian wet sclerophyll forests. We hypothesize that both the phyto- and mycobiont, mantle type, soil microbiotope and geographical distance affect the diversity and occurrence of the associated ascomycetes. Using the culture-independent rDNA sequence analysis, we demonstrate a high diversity of these fungi on different hosts and habitats. Plant host has the strongest effect on the occurrence of the dominant species and community composition of ectomycorrhiza-associated fungi. Root endophytes, soil saprobes, myco-, phyto- and entomopathogens contribute to the ectomycorrhizaassociated ascomycete community. Taxonomically these Ascomycota mostly belong to the orders Helotiales, Hypocreales, Chaetothyriales and Sordariales. Members of Helotiales from both Tasmania and the Northern Hemisphere are phylogenetically closely related to root endophytes and ericoid mycorrhizal fungi, suggesting their strong ecological and evolutionary links. Ectomycorrhizal mycobionts from Australia and the Northern Hemisphere are taxonomically unrelated to each other and phylogenetically distant to other helotialean root-associated fungi, indicating independent evolution. The ubiquity and diversity of the secondary root-associated fungi should be considered in studies of mycorrhizal communities to avoid overestimating the richness of true symbionts.

Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (www.kew.org/genomesize/homepage. html), the Animal Genome Size Database (www. genomesize.com) and the Fungal Genome Size Database (www.zbi.ee/fungal-genomesize/). In total, these databases provide freely accessible genome size data for >10 000 species of eukaryotes assembled from more than 50 years’ worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundamental features of genome structure, for genomics-based comparative biodiversity studies, and as direct estimators of the cost of complete sequencing programs.