Lepidostromatales, a new order of lichenized fungi (Basidiomycota, Agaricomycetes), with two new genera, Ertzia and Sulzbacheromyces, and one new species, Lepidostroma winklerianum

Morphological characteristics and phylogenetic analyses revealed four new wood inhabiting fungi (Agaricomycetes, Basidiomycota) in Xizang Autonomous Region, China

Four new fungi from Xizang in southwest China, Caloceraramaria, Ceraceomycesrhizomorphus, Leptosporomyceslinzhiensis, and Ramariaxizangensis are described and illustrated based on the morphological and molecular evidence. Caloceraramaria is characterized by the ramal and bright orange basidiomata, a monomitic hyphal system with simple septa generative hyphae, usually 4-septate basidiospores; Ceraceomycesrhizomorphus is characterized by the cream to yellowish basidiomata with rhizomorphs, cylindrical basidiospores; Leptosporomyceslinzhiensis is characterized by white with pink basidiomata, cylindrical to oblong ellipsoid basidiospores; Ramariaxizangensis is characterized by flesh pink basidiomata, branched dichotomously in 4-5 ranks, a monomitic hyphal system with clamped generative hyphae, ellipsoid to cylindrical and densely warted basidiospores.

Family matters inside the order Agaricales: systematic reorganization and classification of incertae sedis clitocyboid, pleurotoid and tricholomatoid taxa based on an updated 6-gene phylogeny

The phylogenetic position of several clitocyboid/pleurotoid/tricholomatoid genera previously considered incertae sedis is here resolved using an updated 6-gene dataset of Agaricales including newly sequenced lineages and more complete data from those already analyzed before. Results allowed to infer new phylogenetic relationships, and propose taxonomic novelties to accommodate them, including up to ten new families and a new suborder. Giacomia (for which a new species from China is here described) forms a monophyletic clade with Melanoleuca (Melanoleucaceae) nested inside suborder Pluteineae, together with the families Pluteaceae, Amanitaceae (including Leucocortinarius), Limnoperdaceae and Volvariellaceae. The recently described family Asproinocybaceae is shown to be a later synonym of Lyophyllaceae (which includes also Omphaliaster and Trichocybe) within suborder Tricholomatineae. The families Biannulariaceae, Callistosporiaceae, Clitocybaceae, Fayodiaceae, Macrocystidiaceae (which includes Pseudoclitopilus), Entolomataceae, Pseudoclitocybaceae (which includes Aspropaxillus), Omphalinaceae (Infundibulicybe and Omphalina) and the new families Paralepistaceae and Pseudoomphalinaceae belong also to Tricholomatineae. The delimitation of the suborder Pleurotineae (= Schizophyllineae) is discussed and revised, accepting five distinct families within it, viz. Pleurotaceae, Cyphellopsidaceae, Fistulinaceae, Resupinataceae and Schizophyllaceae. The recently proposed suborder Phyllotopsidineae (= Sarcomyxineae) is found to encompass the families Aphroditeolaceae, Pterulaceae, Phyllotopsidaceae, Radulomycetaceae, Sarcomyxaceae (which includes Tectella), and Stephanosporaceae, all of them unrelated to Pleurotaceae (suborder Pleurotineae) or Typhulaceae (suborder Typhulineae). The new family Xeromphalinaceae, encompassing the genera Xeromphalina and Heimiomyces, is proposed within Marasmiineae. The suborder Hygrophorineae is here reorganized into the families Hygrophoraceae, Cantharellulaceae, Cuphophyllaceae, Hygrocybaceae and Lichenomphaliaceae, to homogenize the taxonomic rank of the main clades inside all suborders of Agaricales. Finally, the genus Hygrophorocybe is shown to represent a distinct clade inside Cuphophyllaceae, and the new combination H. carolinensis is proposed. Taxonomic novelties: New suborder: Typhulineae Vizzini, Consiglio & P. Alvarado. New families: Aphroditeolaceae Vizzini, Consiglio & P. Alvarado, Melanoleucaceae Locq. ex Vizzini, Consiglio & P. Alvarado, Paralepistaceae Vizzini, Consiglio & P. Alvarado, Pseudoomphalinaceae Vizzini, Consiglio & P. Alvarado, Volvariellaceae Vizzini, Consiglio & P. Alvarado, Xeromphalinaceae Vizzini, Consiglio & P. Alvarado. New species: Giacomia sinensis J.Z. Xu. Stat. nov.: Cantharellulaceae (Lodge, Redhead, Norvell & Desjardin) Vizzini, Consiglio & P. Alvarado, Cuphophyllaceae (Z.M. He & Zhu L. Yang) Vizzini, Consiglio & P. Alvarado, Hygrocybaceae (Padamsee & Lodge) Vizzini, Consiglio & P. Alvarado, Lichenomphaliaceae (Lücking & Redhead) Vizzini, Consiglio & P. Alvarado. New combination: Hygrophorocybe carolinensis (H.E. Bigelow & Hesler) Vizzini, Consiglio & P. Alvarado. New synonyms: Sarcomyxineae Zhu L. Yang & G.S. Wang, Schizophyllineae Aime, Dentinger & Gaya, Asproinocybaceae T. Bau & G.F. Mou. Incertae sedis taxa placed at family level: Aphroditeola Redhead & Manfr. Binder, Giacomia Vizzini & Contu, Hygrophorocybe Vizzini & Contu, Leucocortinarius (J.E. Lange) Singer, Omphaliaster Lamoure, Pseudoclitopilus Vizzini & Contu, Resupinatus Nees ex Gray, Tectella Earle, Trichocybe Vizzini. New delimitations of taxa: Hygrophorineae Aime, Dentinger & Gaya, Phyllotopsidineae Zhu L. Yang & G.S. Wang, Pleurotineae Aime, Dentinger & Gaya, Pluteineae Aime, Dentinger & Gaya, Tricholomatineae Aime, Dentinger & Gaya. Resurrected taxa: Fayodiaceae Jülich, Resupinataceae Jülich. Citation: Vizzini A, Alvarado P, Consiglio G, Marchetti M, Xu J (2024). Family matters inside the order Agaricales: systematic reorganization and classification of incertae sedis clitocyboid, pleurotoid and tricholomatoid taxa based on an updated 6-gene phylogeny. Studies in Mycology 107: 67-148. doi: 10.3114/sim.2024.107.02.

A new record of Sulzbacheromyces caatingae (Basidiomycota, Agaricomycetes) from Mato Grosso do Sul and a worldwide infrageneric identification key

Sulzbacheromyces is a genus of basidiolichen that includes nine species scattered on the African, American, and Asian continents. Sequences of the universal barcode of Fungi, the nuclear internal transcribed spacer - nuITS region, are available to all known species of the genus. Specimens of Sulzbacheromyces caatingae were collected during two expeditions in the Morro of Paxixi, Mato Grosso do Sul state, Midwest region of Brazil, in the Cerrado biome, where it was reported for the first time to the state. Morphological and anatomical analyses were performed. Specimens from Mato Grosso do Sul have a light green to indistinct thallus, while specimens from Ceará, Paraíba, and Piauí states present a thin green crust on the substrate. The nuITS sequences were also generated, and the distribution of S. caatingae was plotted with the haplotypes. Morphological differences were not reflected in the molecular analysis, which confirmed the identification of the species. In addition, an identification key to the known Sulzbacheromyces species is provided.

Xenasmatellales ord. nov. and Xenasmatellaceae fam. nov. for Xenasmatella (Agaricomycetes, Basidiomycota)

In the era of molecular phylogeny as dominant evidence in fungal taxonomy, the taxonomic framework of fungi adopted from morphological characteristics has been largely updated. Compared with other fungal groups, macrofungi underwent fewer updates at the order and higher level. In this study, the taxonomic placement of a poorly known macro-basidiomycetous genus Xenasmatella is studied. Phylogenetic and molecular clock analyses inferred from a seven-locus dataset support that the genus represents an order rank lineage. Accordingly, a monotypic order Xenasmatellales and a monotypic family Xenasmatellaceae are newly introduced for Xenasmatella within Agaricomycetes. The species diversity and relationships of Xenasmatella are further clarified with the aid of the phylogenetic analysis inferred from a four-locus dataset. In association with morphological characteristics, a new species Xenasmatella hjortstamii is described. Moreover, the distribution of Xenasmatella ailaoshanensis, X. gossypina, and X. wuliangshanensis previously known only from type localities in Yunnan Province, China are expanded. In addition, two unnamed single-specimen lineages of Xenasmatella from Victoria State, Australia and Sichuan, China are revealed, likely representing two potential new species of this genus. In summary, the current study updates the taxonomic framework of Agaricomycetes and provides a crucial supplement for comprehensively understanding the evolutionary history of this fungal class.

Digging Up the Roots: Taxonomic and Phylogenetic Disentanglements in Corticiaceae s.s. (Corticiales, Basidiomycota) and Evolution of Nutritional Modes

Corticiaceae is one of the traditional families of the Agaricomycetes and served for a long time as a convenient placement for basidiomycetes with a resupinate, corticioid form of fruiting body. Molecular studies have helped to assign many corticioid fungi to diverse families and orders; however, Corticiaceae still lacks a phylogenetic characterization and modern circumscription. Here, we provide the first comprehensive phylogenetic and taxonomic revision of the family Corticiaceae based on extensive type studies and sequences of nLSU, ITS, IGS, nSSU, and mtSSU regions. Our analyses support the recognition of ten monophyletic genera in the Corticiaceae, and show that nutritional mode is not a robust basis for generic delimitations in the family. The genus Mycobernardia and the species Corticium thailandicum, Erythricium vernum, and Marchandiomyces allantosporus are described as new to science, and five new combinations are proposed. Moreover, ancestral character state reconstruction revealed that saprotrophy is the plesiomorphic nutritional mode in the Corticiaceae, while several transitions have occurred to diverse nutritional modes in this family. Identification keys are provided to the genera in Corticiaceae s.s. as well as to the species in Corticium, Erythricium, Laetisaria, and Marchandiomyces.

The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.

Fruiting body form, not nutritional mode, is the major driver of diversification in mushroom-forming fungi

With ∼36,000 described species, Agaricomycetes are among the most successful groups of Fungi. Agaricomycetes display great diversity in fruiting body forms and nutritional modes. Most have pileate-stipitate fruiting bodies (with a cap and stalk), but the group also contains crust-like resupinate fungi, polypores, coral fungi, and gasteroid forms (e.g., puffballs and stinkhorns). Some Agaricomycetes enter into ectomycorrhizal symbioses with plants, while others are decayers (saprotrophs) or pathogens. We constructed a megaphylogeny of 8,400 species and used it to test the following five hypotheses regarding the evolution of morphological and ecological traits in Agaricomycetes and their impact on diversification: 1) resupinate forms are plesiomorphic, 2) pileate-stipitate forms promote diversification, 3) the evolution of gasteroid forms is irreversible, 4) the ectomycorrhizal (ECM) symbiosis promotes diversification, and 5) the evolution of ECM symbiosis is irreversible. The ancestor of Agaricomycetes was a saprotroph with a resupinate fruiting body. There have been 462 transitions in the examined morphologies, including 123 origins of gasteroid forms. Reversals of gasteroid forms are highly unlikely but cannot be rejected. Pileate-stipitate forms are correlated with elevated diversification rates, suggesting that this morphological trait is a key to the success of Agaricomycetes. ECM symbioses have evolved 36 times in Agaricomycetes, with several transformations to parasitism. Across the entire 8,400-species phylogeny, diversification rates of ectomycorrhizal lineages are no greater than those of saprotrophic lineages. However, some ECM lineages have elevated diversification rates compared to their non-ECM sister clades, suggesting that the evolution of symbioses may act as a key innovation at local phylogenetic scales.

Multigene phylogeny and taxonomic revision of Atheliales s.l.: Reinstatement of three families and one new family, Lobuliciaceae fam. nov

Atheliales (Agaricomycetes, Basidiomycota) is an order mostly composed of corticioid fungi, containing roughly 100 described species in 20 genera. Members exhibit remarkable ecological diversity, including saprotrophs, ectomycorrhizal symbionts, facultative parasites of plants or lichens, and symbionts of termites. Ectomycorrhizal members are well known because they often form a major part of boreal and temperate fungal communities. However, Atheliales is generally understudied, and molecular data are scarce. Furthermore, the order is riddled with many taxonomic problems; some genera are non-monophyletic and several species have been shown to be more closely related to other orders. We investigated the phylogenetic position of genera that are currently listed in Atheliales sensu lato by employing an Agaricomycetes-wide dataset with emphasis on Atheliales including the type species of genera therein. A phylogenetic analysis based on 5.8S, LSU, rpb2, and tef1 (excluding third codon) retrieved Atheliales in subclass Agaricomycetidae, as sister to Lepidostromatales. In addition, a number of Atheliales genera were retrieved in other orders with strong support: Byssoporia in Russulales, Digitatispora in Agaricales, Hypochnella in Polyporales, Lyoathelia in Hymenochaetales, and Pteridomyces in Trechisporales. Based on this result, we assembled another dataset focusing on the clade with Atheliales sensu stricto and representatives from Lepidostromatales and Boletales as outgroups, based on ITS (ITS1-5.8S-ITS2), LSU, rpb2, and tef1. The reconstructed phylogeny of Atheliales returned five distinct lineages, which we propose here as families. Lobulicium, a monotypic genus with a distinct morphology of seven-lobed basidiospores, was placed as sister to the rest of Atheliales. A new family is proposed to accommodate this genus, Lobuliciaceae fam. nov. The remaining four lineages can be named following the family-level classification by Jülich (1982), and thus we opted to use the names Atheliaceae, Byssocorticiaceae, Pilodermataceae, and Tylosporaceae, albeit with amended circumscriptions.

Continental-scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria

PREMISE

Motivated to make sensible interpretations of the massive volume of data from the Australian Microbiome Initiative (AusMic), we characterize the soil mycota of Australia. We establish operational taxonomic units (OTUs) from the data and compare these to GenBank and a data set from the National Herbarium of Victoria (MEL), Melbourne, Australia. We also provide visualizations of Agaricomycete diversity, drawn from our analyses of the AusMic sequences and taxonomy.

METHODS

The AusMic internal transcribed spacer (ITS) data were filtered to create OTUs, which were searched against the National Center for Biotechnology Information Nucleotide database and the MEL database. We further characterized a portion of our OTUs by graphing the counts of the families and orders of Agaricomycetes. We also graphed AusMic species determinations for Australian Agaricomycetes against latitude.

RESULTS

Our filtering process generated 192,325 OTUs; for Agaricomycetes, there were 27,730 OTUs. Based on the existing AusMic taxonomy at species level, we inferred the diversity of Australian Agaricomycetes against latitude to be lowest between -20 and -25 decimal degrees.

DISCUSSION

BLAST comparisons provided reciprocal insights between the three data sets, including the detection of unusual root-associated species in the AusMic data, insights into mushroom morphology from the MEL data, and points of comparison for the taxonomic determinations between AusMic, GenBank, and MEL. This study provides a tabulation of Australian fungi, different visual snapshots of a subset of those taxa, and a springboard for future studies.

Brazilian fungal diversity represented by DNA markers generated over 20 years

Molecular techniques using fungal DNA barcoding (ITS) and other markers have been key to identifying the biodiversity of different geographic areas, mainly in megadiverse countries. Here, we provide an overview of the fungal diversity in Brazil based on DNA markers of phylogenetic importance generated since 1996. We retrieved fungal sequences of ITS, LSU, SSU, tef1-α, β-tubulin, rpb1, rpb2, actin, chitin synthase, and ATP6 from GenBank using different field keywords that indicated their origin in Brazil. A total of 19,440 sequences were recovered. ITS is the most representative marker (11,209 sequences), with 70.1% belonging to Ascomycota, 18.6% Basidiomycota, 10.2% unidentified, 1.1% Mucoromycota, two sequences of Olpidium bornovanus (Fungi incertae sedis), one sequence of Blastocladiomycota (Allomyces arbusculus), and one sequence of Chytridiomycota (Batrachochytrium dendrobatidis). Considering the sequences of all selected markers, only the phyla Cryptomycota and Entorrhizomycota were not represented. Based on ITS, using a cutoff of 98%, all sequences comprise 3047 OTUs, with the majority being Ascomycota (2088 OTUs) and Basidiomycota (681 OTUs). Previous numbers based mainly on morphological and bibliographical data revealed 5264 fungal species from Brazil, with a predominance of Basidiomycota (2741 spp.) and Ascomycota (1881 spp.). The unidentified ITS sequences not assigned to a higher taxonomic level represent 1.61% of all ITS sequences sampled and correspond to 38 unknown class-level lineages (75% cutoff). A maximum likelihood phylogeny based on LSU illustrates the fungal classes occurring in Brazil.

Notes, outline and divergence times of Basidiomycota

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

Sulzbacheromyces sinensis, an Unexpected Basidiolichen, was Newly Discovered from Korean Peninsula and Philippines, with a Phylogenetic Reconstruction of Genus Sulzbacheromyces

Most of lichens are formed by Ascomycota, less than 1% are lichenized Basidiomycota. The flora investigation of lichenized Ascomycota of South Korea has been well studied in the past three decades; however, prior to this study, none of basidiolichens was discovered. During the recent excursion, an unexpected clavarioid basidiolichen, Sulzbacheromyces sinensis was collected. Morphology and ecology has been recorded in detail. DNA was extracted, and ITS, 18S, 28S nuclear rDNA were generated. In order to further confirm the systematic position of the Korean specimens, maximum likelihood and Bayesian inference analysis including all the species of the order Lepidostromatales were conducted based on the ITS. As a result, the phylogenetic tree of the order Lepidostromatales was reconstructed, which differed from the previous studies. The inferred phylogenetic tree showed that species of Sulzbacheromyces in three different continents (Asia, South Africa and South America) were separated into three clades with support. In this study, the species worldwide distribution map of Lepidostromatales was illustrated, and S. sinensis had a widest distribution range (paleotropical extend to the Sino-Japanese) than other species (paleotropical or neotropical). Prior to this study, the range of distribution, southernmost and northernmost points and the fruiting time of S. sinensis were recorded, and the genus Sulzbacheromyces was firstly reported from Korean peninsula and Philippines.

Circumscription and phylogeny of the Lepidostromatales (lichenized Basidiomycota) following discovery of new species from China and Africa

Based on an exhaustive sampling of all known Lepidostromatales, a lineage of clavarioid lichen-forming basidiomycetes, we assess (i) the phylogenetic affinities of the six Chinese species currently accommodated in Multiclavula (Cantharellales) based on inferences from the 18S and 28S subunits of the nuclear ribosomal DNA repeat and (ii) the phylogenetic structure among Chinese populations of Lepidostromatales, based on the nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS]) regions. Multiclavula fossicola and M. sinensis belong to the Lepidostromatales and are transferred to Sulzbacheromyces. Chinese reports of M. clara and M. vernalis belong to species of Lepidostromatales, and specimens identified as M. mucida belong to the nonlichenized genus Clavaria. Hence, evidence of Multiclavula occurring in China is lacking. Similarly, L. calocerum is excluded from the Chinese flora. The recently described L. asianum should be regarded as conspecific with S. sinensis. Three new species of Sulzbacheromyces are described: S. bicolor and S. yunnanensis from China and S. miomboensis from the Democratic Republic of Congo. Consequently, Sulzbacheromyces is new to Asia and Africa. A worldwide key to the species of Lepidostromatales is provided.

A plant pathology perspective of fungal genome sequencing

The majority of plant pathogens are fungi and many of these adversely affect food security. This mini-review aims to provide an analysis of the plant pathogenic fungi for which genome sequences are publically available, to assess their general genome characteristics, and to consider how genomics has impacted plant pathology. A list of sequenced fungal species was assembled, the taxonomy of all species verified, and the potential reason for sequencing each of the species considered. The genomes of 1090 fungal species are currently (October 2016) in the public domain and this number is rapidly rising. Pathogenic species comprised the largest category (35.5 %) and, amongst these, plant pathogens are predominant. Of the 191 plant pathogenic fungal species with available genomes, 61.3 % cause diseases on food crops, more than half of which are staple crops. The genomes of plant pathogens are slightly larger than those of other fungal species sequenced to date and they contain fewer coding sequences in relation to their genome size. Both of these factors can be attributed to the expansion of repeat elements. Sequenced genomes of plant pathogens provide blueprints from which potential virulence factors were identified and from which genes associated with different pathogenic strategies could be predicted. Genome sequences have also made it possible to evaluate adaptability of pathogen genomes and genomic regions that experience selection pressures. Some genomic patterns, however, remain poorly understood and plant pathogen genomes alone are not sufficient to unravel complex pathogen-host interactions. Genomes, therefore, cannot replace experimental studies that can be complex and tedious. Ultimately, the most promising application lies in using fungal plant pathogen genomics to inform disease management and risk assessment strategies. This will ultimately minimize the risks of future disease outbreaks and assist in preparation for emerging pathogen outbreaks.