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Abstract PremiseThe agaricomycete order Cantharellales contains approximately 1000 species of fungi characterized by diverse morphological forms, ecological guilds, and nutritional modes. Examples include coralloid lichens that form symbioses with unicellular green algae, bulbil‐forming lichenicolous species, corticioid free‐living fungi that degrade dead sources of organic carbon, pathogens that cause plant disease, orchid root endosymbionts, and ectomycorrhizal fungi including popular edible mushrooms. However, evolutionary relationships in the Cantharellales remain poorly understood due to conflicting estimates based on ribosomal DNA loci. MethodsWe constructed a five‐gene phylogeny of the Cantharellales using data from 301 specimens to evaluate family‐level relationships. We used penalized likelihood to estimate divergence times and ancestral state reconstruction to test the hypothesis of multiple independent origins of biotrophic ecologies in the order and whether those transitions are younger than the divergence times of associated plant or lichen hosts. ResultsFour monophyletic families were recovered with strong support: Botryobasidiaceae, Ceratobasidiaceae, Hydnaceae s.l., and Tulasnellaceae, with Hydnaceae containing the greatest species richness and morphological diversity. Our results suggest the Cantharellales diverged during the Carboniferous period with subsequent diversification following the Permian‐Triassic extinction. Ancestral state reconstruction supports a saprotrophic most recent common ancestor with at least three transitions to an ectomycorrhizal ecology, multiple transitions to a lichenicolous habit with one or more subsequent transitions to mutualistic nutritional modes, four transitions to an orchid mycorrhizal ecology, and two transitions to a lichenized lifestyle. ConclusionsThis study represents the first comprehensive examination of the evolution of form and function across this ecologically and morphologically diverse order of fungi. 

ABSTRACT Ectomycorrhizal and saprotrophic fungi respond differently to changing edaphic conditions caused by atmospheric deposition. Within each guild, responses can vary significantly, reflecting the diversity of species and their specific adaptations to environmental changes. Metal contaminants are often deposited onto earth's surface through atmospheric deposition, yet few studies have assessed the relationship between soil metal contamination and fungal communities. The goal of this study was to understand how soil metal contamination and other edaphic factors vary across the spruce‐fir ecosystem in the Southern Appalachians and influence fungal diversity and function. Here, we characterize soil fungal communities using high‐throughput sequencing of the ITS2 gene region and found that higher soil lead (Pb) concentrations were associated with lower fungal diversity. Ectomycorrhizal fungi were less diverse (specifically hydrophilic ectomycorrhizal functional types) at plots with elevated soil Pb concentrations, while saprotrophic fungi were less diverse at plots with elevated soil carbon:nitrogen ratios. Fungal community composition was significantly influenced by pH, Pb, and spatial factors. This study identifies important relationships between fungal diversity and soil Pb concentrations and indicates variable responses of genera within well‐defined ecological guilds. Our work highlights the need to characterize poorly understood taxonomic groups of fungi and their function prior to further environmental degradation. 

Abstract Following disturbances such as wildfires, oak seedlings must form a symbiotic association with mycorrhizal fungi to survive. Wildfires, however, reduce available mycorrhizal fungal propagules in the soil. Ectomycorrhizal (ECM) fungi on oak seedlings sampled in severely burned (7 sites), moderately burned (7 sites), and unburned areas (8 sites) in the Great Smoky Mountains National Park were evaluated 21 months after the 2016 Chimney Tops 2 Wildfire by Sanger sequencing of the nuclear ribosomal DNA internal transcribed spacer region (nrITS; fungal barcode). Sequences were aligned and grouped into Operational Taxonomic Units (OTUs) based on well-supported phylogenetic clades and 98–100% nrITS sequence homology with sequences in GenBank. One hundred seventy-nine root-associated fungi comprising 124 OTUs were recovered after removing duplicates (the same fungus on two or more roots of the same plant). The ECM genusRussulawas the most diverse genus (25 OTUs), followed by theThelephora/Tomentellaclade (18 OTUs),Lactifluus(8 OTUs),Lactarius(4 OTUs), and Laccariaaff.laccata(2 OTUs).RussulaOTUs were identified more frequently on oak roots from burned areas and in burned soils, suggesting that someRussulataxa may have a selective advantage in burned areas. High alpha diversity occurred within each of the burn categories, but little overlap of taxa occurred between burn categories (high beta diversity). Approximately half of the recovered OTUs (100/179 total root-associated fungi = 55.9%) were found on a single plant. Oak seedlings growing in moderately and severely burned areas 21 months after a fire were capable of forming root associations with available fungi. In contrast to the expectation that root-associated fungal diversity would be reduced after a wildfire, diversity 1 year after the Chimney Tops 2 Fire was high with ectomycorrhizalLaccaria,Russulaceae, andThelephoraceaedominating. This study suggests that the availability of ECM fungi post-fire is not a barrier to oak re-establishment. 

Abstract Crepidotusis a genus of common saprotrophic fungi well known especially in the Northern Hemisphere, but distribution patterns of individual species are not sufficiently understood. We redefined a taxonomic circumscription ofCrepidotus cinnamomeusbased on morphological and molecular congruencies between the type material and recent collections. The species is well delimited from other similar and currently accepted species of the genus.Crepidotus cinnamomeuswas found to have a broad holarctic distribution with occurrences in North America, Europe and Asia where it grows on twigs and branches of deciduous trees and shrubs in preferably cold humid habitats. Here we present the first multilocus phylogeny of the genus, including portions of theRPB2gene. Our study highlights the importance of sufficient sampling from broader areas supported by sequence data, which is essential for estimation of species delimitation, distribution and correct name assignment forCrepidotusspecies. 

Abstract Multi‐locus sequence data are widely used in fungal systematic and taxonomic studies to delimit species and infer evolutionary relationships. We developed and assessed the efficacy of a multi‐locus pooled sequencing method using PacBio long‐read high‐throughput sequencing. Samples included fresh and dried voucher specimens, cultures and archival DNA extracts of Agaricomycetes with an emphasis on the order Cantharellales. Of the 283 specimens sequenced, 93.6% successfully amplified at one or more loci with a mean of 3.3 loci amplified. Our method recovered multiple sequence variants representing alleles of rDNA loci and single copy protein‐coding genesrpb1,rpb2 andtef1. Within‐sample genetic variation differed by locus and taxonomic group, with the greatest genetic divergence observed among sequence variants ofrpb2 andtef1 from corticioid Cantharellales. Our method is a cost‐effective approach for generating accurate multi‐locus sequence data coupled with recovery of alleles from polymorphic samples and multi‐organism specimens. These results have important implications for understanding intra‐individual genomic variation among genetic loci commonly used in species delimitation of fungi. 

Summary The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures of the transition to the ECM habit within the hyperdiverse Russulaceae.We present comparative analyses of the genomic architecture and the total and secreted gene repertoires of 18 species across the order Russulales, of which 13 are newly sequenced, including a representative of a saprotrophic member of Russulaceae,Gloeopeniophorella convolvens.The genomes of ECM Russulaceae are characterized by a loss of genes for plant cell wall‐degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of small secreted proteins (SSPs) with TE ‘nests’, or dense aggregations of TEs. Some PCWDEs have been retained or even expanded, mostly in a species‐specific manner. The genome ofG. convolvenspossesses some characteristics of ECM genomes (e.g. loss of some PCWDEs, TE expansion, reduction in secondary metabolism clusters).Functional specialization in ECM decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ECM habit, indicating that changes in genome architecture and gene content may be necessary to prime the evolutionary switch. 

Abstract Agarics (gilled mushrooms) and the order Agaricales include some of the best‐known and most charismatic fungi. However, neither group has had its constituent genera exhaustively compiled in a modern phylogenetic context. To provide that framework, we identified and analyzed 1383 names of genera of agarics (regardless of taxonomic placement) and the Agaricales (regardless of morphology), compiling various data for each name. Including 590 accepted names, the other 793 listed with reasons explaining their disuse, this compendium is intended to be comprehensive at present and phylogenetically up‐to‐date. Data we gathered included type species, continents from which type species were described, accepted synonyms of those species, current family placements, gross macromorphological categories, and sequenced loci (for type specimens, type species, and each genus as a whole). Index Fungorum provided a basis for the data, but much was manually confirmed, augmented, or corrected based on recent literature. Among accepted gilled genera, 82% belonged to the Agaricales; among accepted genera of Agaricales, 67% were gilled. Based on automated searches of GenBank and MycoCosm, 7% of generic names had DNA sequences of their type specimens, 68% had sequences of their type species, and 87% had sequences representing their genus. This leaves an estimated 103 accepted genera entirely lacking molecular data. Some subsets of genera have been sequenced relatively thoroughly (e.g., nidularioid genera and genera described from Europe); others relatively poorly (e.g., cyphelloid genera and genera described from Africa and tropical Asia). We also list nomenclaturally threatened and taxonomically doubtful genus and family names. 

Dermolomais traditionally known as a small genus of agarics classified in the familyTricholomataceae. This study implemented a multilocus phylogeny of six DNA regions to recognize phylogenetic species within the genus. The species concept is reinforced by observations of well-defined morphological characters enhanced by long term sampling effort in Europe and North America. Thirty EuropeanDermolomaspecies are described, including 16 new species from Europe and three from North American. These species are classified into two subgenera morphologically distinguished by spores with positive or negative amyloid reaction. A new genusNeodermolomais introduced for theDermoloma-like speciesN. campestre. Localized or continental-scale species endemicity was confirmed based on studied material, but more inclusive phylogenetic clustering supported a mixture of North American species among the European clades. Of the 22 names validly published from Europe prior to this study, 11 could be assigned to well-definedDermolomaspecies recognized here. Of the remaining 11 names, two were considered representingDermolomaspecies not recorded since their description, and nine were established as later synonyms of other species. Morphological studies ofDermolomaare challenging due to the relatively low number of characters suitable for identification of species. The majority of morphological characters showed continuous variation with high overlap throughout the genus. For this reason, species identification requires an awareness of morphological variability within species, and multiple distinguishing characters need to be combined, and furthermore, often a barcode sequence is needed for a certain identification. Stable isotope analysis inDermolomaof δ¹³C and δ¹⁵N revealed an ecological signature similar to known CHEGD fungi, i.e.ClavariaceaeandHygrocybes.l. This indicates thatDermolomaspecies are biotrophic but neither ectomycorrhizal nor saprotrophic and may form mutualistic root endophytic associations with vascular plants.