Thelephora versatilis and Thelephora pseudoversatilis: two new cryptic species with polymorphic basidiomes inhabiting tropical deciduous and sub-perennial forests of the Mexican Pacific coast

Four New Species and One New Record of Thelephora from China

Species of the genus Thelephora (Thelephorales, Thelephoraceae) are ectomycorrhizal symbionts of coniferous and broad-leaved plants, and some of them are well-known edible mushrooms, making it an exceptionally important group ecologically and economically. However, the diversity of the species from China has not been fully elucidated. In this study, we conducted a phylogenetic analysis based on the internal transcribed spacer (ITS) regions, using Maximum Likelihood and Bayesian analyses, along with morphological observations of this genus. Four new species from China are proposed, viz., T. dactyliophora, T. lacunosa, T. petaloides, and T. pinnatifida. In addition, T. sikkimensis originally described from India is reported for the first time from China. Thelephora dactyliophora, T. pinnatifida, and T. sikkimensis are distributed in subtropical forests and mainly associated with plants of the families Fagaceae and Pinaceae. Thelephora lacunosa and T. petaloides are distributed in tropical to subtropical forests. Thelephora lacunosa is mainly associated with plants of the families Fagaceae and Pinaceae, while T. petaloides is mainly associated with plants of the family Fagaceae. Line drawings of microstructures, color pictures of fresh basidiomes, and detailed descriptions of these five species are provided.

Molecular phylogeny and morphology reveal four new species of Thelephora (Thelephorales, Basidiomycota) from subtropical China, closely related to T. ganbajun

The genus of Thelephora is a group of cosmopolitan ectomycorrhizal fungi with basidiocarps of morphological diversity that has an extremely scarce species reported from the forest ecosystem in China. In this study, phylogenetic analyses of Thelephora species from subtropical China were carried out based on multiple loci including the internal transcribed spacer (ITS) regions, the large subunit of nuclear ribosomal RNA gene (nLSU), and the small subunit of mitochondrial rRNA gene (mtSSU). Maximum likelihood and Bayesian analyses were used to construct the phylogenetic tree. The phylogenetic positions of four new species, Th. aquila, Th. glaucoflora, Th. nebula, and Th. pseudoganbajun, were revealed based on morphological and molecular evidence. Molecular analyses demonstrated that the four new species were closely related to Th. ganbajun and formed a clade with robust support in the phylogenetic tree. Regarding morphology, they share some common morphological characteristics, including flabelliform to imbricate pilei, generative hyphae more or less covered by crystals, and subglobose to irregularly lobed basidiospores (5–8 × 4–7 μm) with tuberculate ornamentation. These new species are described and illustrated and are compared to similar morphological or phylogenetically related species. A key to the new and allied species from China is provided.

A new mushroom hyperaccumulator: Cadmium and arsenic in the ectomycorrhizal basidiomycete Thelephora penicillata

Fruit-bodies of six Thelephora species (Fungi, Basidiomycota, Thelephoraceae) were analyzed for their trace element concentrations. In Thelephora penicillata, extremely high concentrations of Cd and As were found, followed by highly elevated concentrations of Cu and Zn. The highest accumulation ability was found for Cd with a mean concentration of 1.17 ± 0.37 g kg^-1 (dry mass) in fruit-bodies collected from 20 unpolluted sites; the mean As concentration was 0.878 ± 0.242 g kg^-1. Furthermore, striking accumulation of Se (923 ± 28 mg kg^-1) was found in one sample of T. vialis and elevated concentrations of S were detected in T. palmata (19.6 ± 5.9 g kg^-1). The analyzed Thelephora species were sequenced and, based on the Maximum Likelihood phylogenetic analysis (ITS rDNA) of the genus, possible other Thelephora (hyper)accumulators were predicted on the basis of their phylogenetic relationship with the discovered (hyper)accumulators. The striking ability of T. penicillata to accumulate simultaneously Cd, As, Cu, and Zn has no parallel in the Fungal Kingdom and raises the question of a biological importance of metal(loid) hyperaccumulation in mushrooms.

Taxonomy and Phylogeny Reveal Two New Potential Edible Ectomycorrhizal Mushrooms of Thelephora from East Asia

The ectomycorrhizal basidiomycetes genus Thelephora has been understudied in subtropical ecosystems. Many species of Thelephora are important edible and medicinal fungi, with substantial economic value. Two new Thelephora species, T. grandinioides and T. wuliangshanensis spp. nov. are proposed here based on a combination of morphological features and molecular evidence. Thelephora grandinioides is characterized by laterally stipitate basidiocarps with a grandinoid hymenial surface, a monomitic hyphal system with clamped generative hyphae, and the presence of tubular and septated cystidia and subglobose to globose basidiospores measuring as 5.3–7.4 × 4–6.5 µm. Thelephora wuliangshanensis is characterized by infundibuliform basidiocarps, radially black striate on the pileus, a smooth, umber to coffee hymenial surface, a monomitic hyphal system with thick-walled generative hyphae, and basidiospores that turn greenish grey to buff in 5% KOH. Phylogenetic analyses of rDNA internal transcribed spacer region (ITS) and nuclear large subunit region (nrLSU) showed that the two new Thelephora are phylogenetically distinct: T. grandinioides is sister to T. aurantiotincta and T. sikkimensis, while T. wuliangshanensis is sister to a clade comprising T. austrosinensis and T. aurantiotincta with high support as well.

Complete mitochondrial genome of the edible Basidiomycete mushroom Thelephora aurantiotincta (Aphyllophorales: Thelephoraceae) from China

The complete mitochondrial genome of Thelephora aurantiotincta, an edible Basidiomycete mushroom species with ecological and economic value is reported in this study. The whole genome is a circular molecule 50,672 bp in length and encodes 42 genes as follows: 15 protein-coding genes, two rRNA genes and 25 tRNA genes. The A, T, C, G contents in the genome are 35.60%, 35.31%, 13.89%, and 15.20%, respectively. Phylogenetic analysis revealed a close relationship between T. aurantiotincta and T. ganbajun. This is the first complete mitochondrial genome for T. aurantiotincta that will be useful for providing basic genetic information for this important species.

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.

Caryophyllales are the main hosts of a unique set of ectomycorrhizal fungi in a Neotropical dry forest

The ectomycorrhizal symbiosis was long thought to be restricted to temperate forests. However, as tropical forests have been explored, it has become clear that these habitats host unique ectomycorrhizal (ECM) fungi. We have been exploring tropical dry forests (TDF), which are endangered terrestrial ecosystems and hotspots of endemism. Since Fabaceae is the main plant family in this environment, we hypothesized that trees in this lineage would be the main ECM hosts. We sequenced the ITS rDNA region from fungi and both rbcL and trnL cpDNA from plants to identify both symbiotic partners from root tips. The systematic position of each symbiont was confirmed by Bayesian phylogenetic inference. We identified 20 plant species belonging to 10 families that hosted 19 unique ECM fungal species from 5 lineages. Most ECM fungi were associated with Caryophyllales, not with Fabaceae. Achatocarpus and Guapira, the main hosts, are scattered throughout the forest and are not in monodominant patches. The low ECM fungal diversity can be explained by the low density of host plants and their high specificity. Our results indicate that Caryophyllales is an important order of tropical ECM hosts with at least four independent evolutionary lineages that have evolved the ability to form ectomycorrhizae.

Word-wide meta-analysis of Quercus forests ectomycorrhizal fungal diversity reveals southwestern Mexico as a hotspot

Quercus is the most diverse genus of ectomycorrhizal (ECM) host plants; it is distributed in the Northern and Southern Hemispheres, from temperate to tropical regions. However, their ECM communities have been scarcely studied in comparison to those of conifers. The objectives of this study were to determine the richness of ECM fungi associated with oak forests in the Cuitzeo basin in southwestern Mexico; and to determine the level of richness, potential endemism and species similarity among ECM fungal communities associated with natural oak forests worldwide through a meta-analysis. The ITS DNA sequences of ECM root tips from 14 studies were included in the meta-analysis. In total, 1065 species of ECM fungi have been documented worldwide; however, 812 species have been only found at one site. Oak forests in Europe contain 416 species, Mexico 307, USA 285, and China 151. Species with wider distributions are Sebacinaceae sp. SH197130, Amanita subjunquillea, Cenococcum geophilum, Cortinarius decipiens, Russula hortensis, R. risigallina, R. subrubescens, Sebacinaceae sp. SH214607, Tomentella ferruginea, and T. lapida. The meta-analysis revealed (1) that Mexico is not only a hotspot for oak species but also for their ECM mycobionts. (2) There is a particularly high diversity of ECM Pezizales in oak seasonal forests from western USA to southwestern Mexico. (3) The oak forests in southwestern Mexico have the largest number of potential endemic species. (4) Globally, there is a high turnover of ECM fungal species associated with oaks, which indicates high levels of alpha and beta diversity in these communities.

Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi)

BACKGROUND

Fungi are among the most abundant and diverse organisms on Earth. However, a substantial amount of the species diversity, relationships, habitats, and life strategies of these microorganisms remain to be discovered and characterized. One important factor hindering progress is the difficulty in correctly identifying fungi. Morphological and molecular characteristics have been applied in such tasks. Later, DNA barcoding has emerged as a new method for the rapid and reliable identification of species. The nrITS region is considered the universal barcode of Fungi, and the ITS1 and ITS2 sub-regions have been applied as metabarcoding markers. In this study, we performed a large-scale analysis of all the available Basidiomycota sequences from GenBank. We carried out a rigorous trimming of the initial dataset based in methodological principals of DNA Barcoding. Two different approaches (PCI and barcode gap) were used to determine the performance of the complete ITS region and sub-regions.

RESULTS

For most of the Basidiomycota genera, the three genomic markers performed similarly, i.e., when one was considered a good marker for the identification of a genus, the others were also; the same results were observed when the performance was insufficient. However, based on barcode gap analyses, we identified genomic markers that had a superior identification performance than the others and genomic markers that were not indicated for the identification of some genera. Notably, neither the complete ITS nor the sub-regions were useful in identifying 11 of the 113 Basidiomycota genera. The complex phylogenetic relationships and the presence of cryptic species in some genera are possible explanations of this limitation and are discussed.

CONCLUSIONS

Knowledge regarding the efficiency and limitations of the barcode markers that are currently used for the identification of organisms is crucial because it benefits research in many areas. Our study provides information that may guide researchers in choosing the most suitable genomic markers for identifying Basidiomycota species.