A new promising phylogenetic marker to study the diversity of fungal communities: The Glycoside Hydrolase 63 gene

Aromatic Plants and Their Associated Arbuscular Mycorrhizal Fungi Outcompete Tuber melanosporum in Compatibility Assays with Truffle-Oaks

The high value of black truffle recompenses the slow growth of the fungus when established in the field. Adding a secondary crop, such as medicinal and aromatic plants (MAPs), could further enhance the sustainability of truffle production agro-forest systems. The dual cultures of ectomycorrhizal truffle-oak seedlings and MAPs (lavender, thyme, and sage) previously inoculated and non-inoculated with native arbuscular mycorrhizal fungi (AMF), were established to evaluate plant-fungi relationships. After 12 months in a shadehouse, plants' growth, mycorrhizal colonization, and extraradical soil mycelium (both of Tuber melanosporum and AMF) were measured. Overall, truffle-oaks' growth was negatively affected by the presence of MAPs, especially when inoculated with AMF. In turn, the presence of truffle-oaks barely affected the co-cultured MAPs, and only lavenders showed a significant growth reduction. All AMF-inoculated MAPs showed higher shoot and root biomass than non-inoculated ones. Compared to truffle-oaks growing alone, the presence of co-cultured MAPs, especially when they were AMF-inoculated, significantly decreased both the ectomycorrhizas and soil mycelium of T. melanosporum. These results reveal the strong competition between AMF and T. melanosporum and warn about the need for the protection of intercropping plants and their associated symbiotic fungi to avoid reciprocal counterproductive effects in mixed truffle-oak-AMF-MAP plantations.

Taxonomic studies of bluish Mycena (Mycenaceae, Agaricales) with two new species from northern China

Bluish Mycena are rare, but constitute a taxonomically complex group. A total of eight bluish species in four sections have previously been reported from North America, Europe, Oceania and Asia. Two species with a blue pileus, collected in China during our taxonomic study of Mycena s.l., are described here as new to science: Mycenacaeruleogrisea sp. nov. and M.caeruleomarginata sp. nov. Detailed descriptions, line drawings and a morphological comparison with closely-related species, especially herbarium specimens of M.subcaerulea from the USA, are provided. The results of Bayesian Inference and Maximum Likelihood phylogenetic analyses of a dataset of 96 nuclear rDNA ITS and 20 nLSU sequences of 43 Mycena species are also presented. The morphological data and the results of the phylogenetic analyses support the introduction of M.caeruleogrisea and M.caeruleomarginata as new species. A taxonomic key to bluish Mycena species of sections Amictae, Cyanocephalae, Sacchariferae and Viscipelles is provided.

Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples

Metabarcoding is an important tool for understanding fungal communities. The internal transcribed spacer (ITS) rDNA is the accepted fungal barcode but has known problems. The large subunit (LSU) rDNA has also been used to investigate fungal communities but available LSU metabarcoding primers were mostly designed to target Dikarya (Ascomycota + Basidiomycota) with little attention to early diverging fungi (EDF). However, evidence from multiple studies suggests that EDF comprise a large portion of unknown diversity in community sampling. Here, we investigate how DNA marker choice and methodological biases impact recovery of EDF from environmental samples. We focused on one EDF lineage, Zoopagomycota, as an example. We evaluated three primer sets (ITS1F/ITS2, LROR/LR3, and LR3 paired with new primer LR22F) to amplify and sequence a Zoopagomycota mock community and a set of 146 environmental samples with Illumina MiSeq. We compared two taxonomy assignment methods and created an LSU reference database compatible with AMPtk software. The two taxonomy assignment methods recovered strikingly different communities of fungi and EDF. Target fragment length variation exacerbated PCR amplification biases and influenced downstream taxonomic assignments, but this effect was greater for EDF than Dikarya. To improve identification of LSU amplicons we performed phylogenetic reconstruction and illustrate the advantages of this critical tool for investigating identified and unidentified sequences. Our results suggest much of the EDF community may be missed or misidentified with "standard" metabarcoding approaches and modified techniques are needed to understand the role of these taxa in a broader ecological context.

Significance of incongruent DNA loci in the taxonomy of wood-decaying Basidioradulum radula

Modern taxonomic studies of Agaricomycetes rely on the integrative analyses of morphology, environmental data, geographic distribution, and usually several DNA loci. However, sampling and selection of DNA loci for the analyses are commonly shallow. In this study, we suggest minimal numbers of necessary specimens to sample and DNA loci to analyze in order to prevent inadequate taxonomic decisions in species groups with minor morphological and genealogical differences. We sampled four unlinked nuclear DNA gene regions (nuc rDNA ITS1-5.8S-ITS2, gh63, rpb2, and tef1) to revise the systematics of a common wood-decaying species Basidioradulum radula (Hymenochaetales) on an intercontinental set of specimens collected in the Northern Hemisphere. The DNA loci analyzed violate the genealogical concordance phylogenetic species recognition principles, thus confirming a single-species interpretation. We conclude that Hyphodontia syringae is a younger synonym of B. radula.

Distinct mechanisms shape soil bacterial and fungal co-occurrence networks in a mountain ecosystem

Understanding microbial network assembly is a promising way to predict potential impacts of environmental changes on ecosystem functions. Yet, soil microbial network assembly in mountain ecosystems and its underlying mechanisms remain elusive. Here, we characterized soil microbial co-occurrence networks across 12 altitudinal sites in Mountain Gongga. Despite differences in habitats, soil bacterial networks separated into two different clusters by altitude, namely the lower and higher altitudes, while fungi did not show such a pattern. Bacterial networks encompassed more complex and closer relationships at the lower altitudes, while fungi had closer relationships at the higher altitudes, which could be attributed to niche differentiation caused by high variations in soil environments and plant communities. Both abiotic and biotic factors (e.g. soil pH and bacterial community composition) shaped bacterial networks. However, biotic factors played more important roles than the measured abiotic factors for fungal network assembly. Further analyses suggest that multiple mechanisms including niche overlap/differentiation, cross-feeding and competition between microorganisms could play important roles in shaping soil microbial networks. This study reveals microbial co-occurrence networks in response to different ecological factors, which provides important insights into our comprehensive understanding of microbial network assembly and their functional potentials in mountain ecosystems.

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.

Clitopilus lampangensis (Agaricales, Entolomataceae), a new species from northern Thailand

A new species of agaricomycetes, Clitopiluslampangensis, is described based on collections from northern Thailand. This species was distinguished from previously described Clitopilus species by its pale yellow to grayish yellow pileus with the presence of wider caulocystidia. Molecular phylogenetic analyses, based on the data of the internal transcribed spacers (ITS) and the large subunit (LSU) of the nuclear ribosomal DNA, and the second largest subunit of RNA polymerase II (rbp2) genes, also support the finding that C.lampangensis is distinct from other species within the genus Clitopilus. A full description, color photographs, illustrations and a phylogenetic tree showing the position of C.lampangensis are provided.

Plant-necrotroph co-transcriptome networks illuminate a metabolic battlefield

A central goal of studying host-pathogen interaction is to understand how host and pathogen manipulate each other to promote their own fitness in a pathosystem. Co-transcriptomic approaches can simultaneously analyze dual transcriptomes during infection and provide a systematic map of the cross-kingdom communication between two species. Here we used the Arabidopsis-B. cinerea pathosystem to test how plant host and fungal pathogen interact at the transcriptomic level. We assessed the impact of genetic diversity in pathogen and host by utilization of a collection of 96 isolates infection on Arabidopsis wild-type and two mutants with jasmonate or salicylic acid compromised immunities. We identified ten B. cinereagene co-expression networks (GCNs) that encode known or novel virulence mechanisms. Construction of a dual interaction network by combining four host- and ten pathogen-GCNs revealed potential connections between the fungal and plant GCNs. These co-transcriptome data shed lights on the potential mechanisms underlying host-pathogen interaction.