Early-diverging wood-decaying fungi detected using three complementary sampling methods

Campanophyllummicrosporum (Agaricales, Agaricomycetes), Caloceramultiramosa, and Dacrymycesnaematelioides (Dacrymycetales, Dacrymycetes), three new species from Yunnan Province, southwestern China

Three new species belonging to Basidiomycota from southwestern China are described based on morphological and molecular data. Campanophyllummicrosporum is morphologically characterized by dorsally pseudostipitate, pale orange to brownish orange pileus, excentric to lateral pseudostipe, crowded lamellae, cylindrical-ellipsoid basidiospores 3.0-4.2 × 1.7-2.2 µm, narrowly clavate to clavate basidia 14.5-23.0 × 3.0-4.2 µm, and cylindrical to clavate cheilocystidia 22.0-55.0 × 5.0-10.8 µm. Caloceramultiramosa is morphologically characterized by stipitate, yellowish to orange, dendroid, and dichotomously branched basidiomata, cylindrical to clavate basidia 36.5-52.5 × 3.8-6.1 µm, navicular or reniform, 1-5-septate mature basidiospores 10.4-16.7 × 5.2-7.4 µm. Dacrymycesnaematelioides is morphologically characterized by stipitate and cerebriform, orange to light brown basidiomata, cylindrical to clavate, smooth or roughened basidia 38.5-79.5 × 6.5-10.6 µm, broadly and elliptic-fusiform, 7-septate mature basidiospores 18.5-28.6 × 8.9-13.8 µm. These three new species are supported by the phylogenetic analyses using maximum likelihood (ML) and Bayesian inference (BI) analyses with combined nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) and large ribosomal subunit (LSU) sequences. Full descriptions and photographs of these new species are provided.

Surveying lichen diversity in forests: A comparison of expert mapping and eDNA metabarcoding of bark surfaces

Lichens are an important part of forest ecosystems, contributing to forest biodiversity, the formation of micro-niches and nutrient cycling. Assessing the diversity of lichenised fungi in complex ecosystems, such as forests, requires time and substantial skills in collecting and identifying lichens. The completeness of inventories thus largely depends on the expertise of the collector, time available for the survey and size of the studied area. Molecular methods of surveying biodiversity hold the promise to overcome these challenges. DNA barcoding of individual lichen specimens and bulk collections is already being applied; however, eDNA methods have not yet been evaluated as a tool for lichen surveys. Here, we assess which species of lichenised fungi can be detected in eDNA swabbed from bark surfaces of living trees in central European forests. We compare our findings to an expert floristic survey carried out in the same plots about a decade earlier. In total, we studied 150 plots located in three study regions across Germany. In each plot, we took one composite sample based on six trees, belonging to the species Fagussylvatica, Piceaabies and Pinussylvestris. The eDNA method yielded 123 species, the floristic survey 87. The total number of species found with both methods was 167, of which 48% were detected only in eDNA, 26% only in the floristic survey and 26% in both methods. The eDNA contained a higher diversity of inconspicuous species. Many prevalent taxa reported in the floristic survey could not be found in the eDNA due to gaps in molecular reference databases. We conclude that, currently, eDNA has merit as a complementary tool to monitor lichen biodiversity at large scales, but cannot be used on its own. We advocate for the further development of specialised and more complete databases.

Dendrodacrys: a new genus for species with branched hyphidia in Dacrymyces s.l., with the description of four new species

A new genus named Dendrodacrys is proposed for a monophyletic group in Dacrymycetaceae, containing species with pulvinate to depressed basidiocarps, distinctly branched hymenial hyphidia, and up to 3-septate mature basidiospores. Four taxa in this group, occurring in Europe, are proposed as new species, viz. De. ciprense, De. concrescens, De. ellipsosporum, and De. oblongisporum, based both on morphological and DNA data (nrDNA, RPB1, RPB2, TEF-1α, 12S). These new species are all described in detail, illustrated, and compared with other published taxa that with which they can be confounded. The new combination De. paraphysatum is proposed after revising the type material of Dacrymyces paraphysatus, but other combinations or potentially new non-European species descriptions are postponed pending further studies of additional specimens.

Citation: Zamora JC, Savchenko A, González-Cruz Á, Prieto-García F, Olariaga I, Ekman S (2022). Dendrodacrys: a new genus for species with branched hyphidia in Dacrymyces s.l., with the description of four new species. Fungal Systematics and Evolution9: 27–42. doi: 10.3114/fuse.2022.09.04

Revision of Cerinomyces (Dacrymycetes, Basidiomycota) with notes on morphologically and historically related taxa

Cerinomyces (Dacrymycetes, Basidiomycota) is a genus traditionally defined by corticioid basidiocarps, in contrast to the rest of the class, which is characterized by gelatinous ones. In the traditional circumscription the genus is polyphyletic, and the monotypic family Cerinomycetaceae is paraphyletic. Aiming for a more concise delimitation, we revise Cerinomyces s.l. with a novel phylogeny based on sequences of nrDNA (SSU, ITS, LSU) and protein-coding genes (RPB1, RPB2, TEF1-α). We establish that monophyletic Cerinomyces s.s. is best characterized not by the corticioid morphology, but by a combination of traits: hyphal clamps, predominantly aseptate thin-walled basidiospores, and low content of carotenoid pigments. In our updated definition, Cerinomyces s.s. encompasses five well-supported phylogenetic clades divided into two morphological groups: (i-iii) taxa with arid corticioid basidiocarps, including the generic type C. pallidus; and (iv-v) newly introduced members with gelatinous basidiocarps, like Dacrymyces enatus and D. tortus. The remaining corticioid species of Cerinomyces s.l. are morphologically distinct and belong to the Dacrymycetaceae: our analysis places the carotenoid-rich Cerinomyces canadensis close to Femsjonia, and we transfer the clamps-lacking C. grandinioides group to Dacrymyces. In addition, we address genera related to Cerinomyces s.l. historically and morphologically, such as Ceracea, Dacryonaema and Unilacryma. Overall, we describe twenty-four new species and propose nine new combinations in both Cerinomycetaceae and Dacrymycetaceae.

Meta-analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost-effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta-analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently "better."Environmental DNA publications for multiple species or single macro-organism detection were identified using the Web of Science, by searching "eDNA" and "environmental DNA" across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa-dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance. Synthesis and applications: The results of this meta-analysis demonstrate that where there is a direct comparison, eDNA surveys of macro-organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution against the use of qualitative statements about relative performance. This consistency and rigor will simplify how the eDNA research community tracks methods-based advances and will also provide greater clarity for conservation practitioners. To this end suggest reporting standards for eDNA studies.

Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov

We present a multilocus phylogeny of the class Dacrymycetes, based on data from the 18S, ITS, 28S, RPB1, RPB2, TEF-1α, 12S, and ATP6 DNA regions, with c. 90 species including the types of most currently accepted genera. A variety of methodological approaches was used to infer phylogenetic relationships among the Dacrymycetes, from a supermatrix strategy using maximum likelihood and Bayesian inference on a concatenated dataset, to coalescence-based calculations, such as quartet-based summary methods of independent single-locus trees, and Bayesian integration of single-locus trees into a species tree under the multispecies coalescent. We evaluate for the first time the taxonomic usefulness of some cytological phenotypic characters, i.e., vacuolar contents (vacuolar bodies and lipid bodies), number of nuclei of recently discharged basidiospores, and pigments, with especial emphasis on carotenoids. These characters, along with several others traditionally used for the taxonomy of this group (basidium shape, presence and morphology of clamp connections, morphology of the terminal cells of cortical/marginal hyphae, presence and degree of ramification of the hyphidia), are mapped on the resulting phylogenies and their evolution through the class Dacrymycetes discussed. Our analyses reveal five lineages that putatively represent five different families, four of which are accepted and named. Three out of these four lineages correspond to previously circumscribed and published families (Cerinomycetaceae, Dacrymycetaceae, and Unilacrymaceae), and one is proposed as the new family Dacryonaemataceae. Provisionally, only a single order, Dacrymycetales, is accepted within the class. Furthermore, the systematics of the two smallest families, Dacryonaemataceae and Unilacrymaceae, are investigated to the species level, using coalescence-based species delimitation on multilocus DNA data, and a detailed morphological study including morphometric analyses of the basidiospores. Three species are accepted in Dacryonaema, the type, Da. rufum, the newly combined Da. macnabbii (basionym Dacrymyces macnabbii), and a new species named Da. macrosporum. Two species are accepted in Unilacryma, the new U. bispora, and the type, U. unispora, the latter treated in a broad sense pending improved sampling across the Holarctic.

Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms

Among terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, however the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. Herein, we sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-decaying mushrooms Dacrymycetes, using an approach that combines fruiting-body collection, culture isolation, and environmental DNA (eDNA) metabarcoding of decaying branches. Among the 28 operational taxonomic units (OTUs) detected during a three-year investigation, 10 each were from fruiting bodies and cultured mycelia and 27 were detected as eDNA sequences. eDNA metabarcoding revealed various lineages across the Dacrymycetes phylogeny. Alternatively, fruiting-body and culture surveys uncovered only ~50% of the OTUs detected through eDNA metabarcoding, suggesting that several inconspicuous or difficult-to-isolate strains are latent in the environment. Further, eDNA and culture surveys revealed early-diverging clades that were not identified in the fruiting-body survey. Thus, eDNA and culture-based techniques can uncover inconspicuous yet phylogenetically important mushroom lineages that may otherwise be overlooked via typical visual investigations.

Identification and control of wood-deteriorating fungi

ABSTRACT: Wood is rich in organic compounds; thus, it is susceptible to attacks by several deteriorating agents because they acknowledge such attacks as a necessary energy supply. Fungi stand out among these agents since they can attack the wood in trees (before felling) and in several post-felling stages. Fungi are biological agents that use organic compounds as food sources, and that is the reason why they degrade most chemical components found in wood. Wood attacked by fungi suffers significant value loss, since these degrading agents affect their mechanical and aesthetic properties. Fungi — which are classified as staining, molding and rotting — are one of the main responsible for the biggest losses in the timber industry. Wood can be virtually used in a whole range of environments, a fact that makes it susceptible to attacks by different fungal species, since the ideal conditions for fungal development change from species to species. In other words, the fact that one or more fungal species are capable of deteriorating wood is directly related to conditions wood is subjected to. Thus, it is essential knowing how to evaluate fungal attacks, symptoms to be taken into consideration at the time to identify the type of attacking organism and the attack stage, as well as the control and prevention measures to be applied to these organisms.

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a 'Third Kingdom', embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum-level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.

Leveraging single-cell genomics to expand the fungal tree of life

Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across the fungal tree of life using a new single-cell genomics pipeline. We show that, despite a large variation in genome and gene space recovery from each single amplified genome (SAG), ≥90% can be recovered by combining multiple SAGs. SAGs provide robust placement for early-diverging lineages and infer a diploid ancestor of fungi. Early-diverging fungi share metabolic deficiencies and show unique gene expansions correlated with parasitism and unculturability. Single-cell genomics holds great promise in exploring fungal diversity, life cycles and metabolic potential.

Phylogenetic relationships of eight new Dacrymycetes collected from New Zealand

Dacrymycetes, sister to Agaricomycetes, is a noteworthy lineage for studying the evolution of wood-decaying basidiomycetes; however, its species diversity and phylogeny are largely unknown. Species of Dacrymycetes previously used in molecular phylogenetic analyses are mainly derived from the Northern Hemisphere, thus insufficient knowledge exists concerning the Southern Hemisphere lineages. In this study, we investigated the species diversity of Dacrymycetes in New Zealand. We found 11 previously described species, and eight new species which were described here: Calocera pedicellata, Dacrymyces longistipitatus, D. pachysporus, D. stenosporus, D. parastenosporus, D. cylindricus, D. citrinus, and D. cyrtosporus. These eight newly described species and seven of the known ones, namely, Calocera fusca, C. cf. guepinioides, C. lutea, Dacrymyces flabelliformis, D. intermedius, D. subantarcticensis, and Heterotextus miltinus, have rarely or never been recorded from the Northern Hemisphere. In a molecular-based phylogeny, these New Zealand strains were scattered throughout the Dacrymycetaceae clade. Sequences obtained from specimens morphologically matching C. guepinioides were separated into three distant clades. Because no obvious morphological differences could be discerned between the specimens in each clade and no sequence exists from the type specimen, a C. guepinioides s.str. clade could not be determined. This survey of dacrymycetous species in the Southern Hemisphere has increased taxon sampling for phylogenetic analyses that can serve as a basis for the construction of a stable classification of Dacrymycetes.