Irja Saar

Towards a unified paradigm for sequence‐based identification of fungi

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third‐party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web‐based sequence management system in UNITE.

Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers.

Ectomycorrhizal (ECM) symbiosis is a widespread plant nutrition strategy in Australia, especially in semiarid regions. This study aims to determine the diversity, community structure and host preference of ECM fungi in a Tasmanian wet sclerophyll forest. Ectomycorrhizal fungi were identified based on anatomotyping and rDNA internal transcribed spacer (ITS)-large subunit (LSU) sequence analysis using taxon-specific primers. Host tree roots were identified based on root morphology and length differences of the chloroplast trnL region. A total of 123 species of ECM fungi were recovered from root tips of Eucalyptus regnans (Myrtaceae), Pomaderris apetala (Rhamnaceae) and Nothofagus cunninghamii (Nothofagaceae). The frequency of two thirds of the most common ECM fungi from several lineages was significantly influenced by host species. The lineages of Cortinarius, Tomentella-Thelephora, Russula-Lactarius, Clavulina, Descolea and Laccaria prevailed in the total community and their species richness and relative abundance did not differ by host species. This study demonstrates that strongly host-preferring, though not directly specific, ECM fungi may dominate the below-ground community. Apart from the richness of Descolea, Tulasnella and Helotiales and the lack of Suillus-Rhizopogon and Amphinema-Tylospora, the ECM fungal diversity and phylogenetic community structure is similar to that in the Holarctic realm.

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee.

Ectomycorrhizas of Coltricia and Coltriciella (Hymenochaetales, Basidiomycota) on Caesalpiniaceae, Dipterocarpaceae and Myrtaceae in Seychelles

Ectomycorrhizal fungi, especially basidiomycetes, have repeatedly evolved from saprotrophic ancestors. Using rDNA internal transcribed spacer and large subunit sequences, we demonstrate that four species of Coltricia and Coltriciella form ectomycorrhiza with the native Vateriopsis seychellarum (Dipterocarpaceae) and Intsia bijuga (Caesalpiniaceae) as well as the introduced Eucalyptus robusta (Myrtaceae) in Seychelles. Coltricia and Coltriciella species share a thin, orange-brown to dark brown mantle and extremely thick, clampless hyphae. Phylogenetic analyses placed Coltriciella monophyletic within Coltricia. This study provides further evidence that fruiting habit on dead wood does not indicate saprotrophic lifestyle.

The phylogeny and taxonomy of genera Cystoderma and Cystodermella (Agaricales) based on nuclear ITS and LSU sequences

Species delimitation in Cystoderma and Cystodermella was evaluated based on ITS and LSU rDNA sequences as well as morphological data. Two species of Cystoderma are synonymised with C. carcharias and three species with C. jasonis, distinguishing the synonymised taxa as varieties of these accepted species. Analyses of partial LSU rDNA sequences revealed Cystoderma and Cystodermella as distinct monophyletic genera, with Ripartitella representing a well-supported sister group of the latter. Phaeolepiota aurea represents either an unsupported sister group or member of Cystoderma in the phylogenies based on LSU and ITS sequences rDNA data, respectively. The tribe Cystodermateae sensu Singer did not appear monophyletic according to analyses of LSU sequences. On the basis of these data, the phylogenetic relationships among most of the analyzed genera could not be resolved unequivocally.

Phylogenetic taxonomy of Hymenochaete and related genera (Hymenochaetales)

Species delimitation in Hymenochaete sensu lato was evaluated based on partial nucLSU rDNA sequences, isoenzyme analyses and morphological data. Analyses of LSU data revealed Hymenochaete sensu stricto and Pseudochaete as distinct monophyletic genera. Transfer of Hydnochaete olivacea into genus Pseudochaete and Dichochaete setosa into genus Hymenochaete (as H. resupinata) was supported by the results of molecular analyses. A new species Hymenochaete koeljalgii from Tanzania was described. The species of genus Hymenochaete sensu stricto were divided into four well-supported clades possessing no distinctive morphological characters.

Type studies of two Tricholomopsis species described by Peck

A study of the types of two species of Tricholomopsis described by C. H. Peck, T. flavescens and T. sulphureoides, revealed that their ITS sequences differ clearly from each other and from previously studied European species. The species T. osiliensis described from Estonia is a synonym of T. sulphureoides. Because both type collections were mixed, lectotypes were designated for each.

North American matsutake: names clarified and a new species described

ABSTRACT Tricholoma matsutake, known widely as “matsutake,” has great commercial and cultural significance in Japan. Because Japanese production is insufficient to meet the high domestic demand, morphologically similar mushrooms, thought by many to belong to T. magnivelare, are imported from western North America. However, molecular data produced since the early 2000s have indicated that more than one species of matsutake occur in North America and this raises the question of correct naming for the different species. To address this question, we assessed the phylogenetic diversity within North American matsutake based on nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS] barcode) sequences, including newly obtained sequences from the type collections for Agaricus ponderosus and Armillaria arenicola, and morphological characters. Our results agree with earlier indications that three matsutake species occur in North America and allow us to clarify the correct application of names—T. magnivelare from the eastern USA and Canada, T. murrillianum from the western USA and Canada, and T. mesoamericanum from Mexico, newly described here. The existence of the three North American species is further supported by the results of evolutionary divergence analysis, geographical distributions, and morphological characters.

Polyozellus multiplex (Thelephorales) is a species complex containing four new species

ABSTRACT Geographic, morphological, and internal transcribed spacer (ITS)-based molecular review of collections identified as Polyozellus multiplex revealed that it is a complex of five phylogenetic species. Average spore size—either less or more than 7 × 6 µm—splits the complex into a small-spored group of two (P. multiplex and P. atrolazulinus) and a large-spored group of three (P. mariae, P. marymargaretae, and P. purpureoniger). Basidiocarps of the small-spored species are somewhat smaller than the large-spored ones, are various shades of blue, dark all the way to black, with brownish tomentum only in early growth, have dark context, and have pilei that tend to flare out at the edge. The large-spored species produce somewhat larger sporocarps, have light or lighter context than the pileipelis, and usually retain some brown on the mature pileipellis, the edge of which tends to curl like a cabbage leaf. All will darken or blacken with age. The species of the P. multiplex complex are distributed in the northern coniferous region, with the exception of Europe. One species (P. atrolazulinus) is known from three regions, eastern Asia, western North America, and northeastern North America. Two species are known from two regions: P. purpureoniger in eastern Asia and northwestern North America and P. multiplex in eastern Asia and eastern North America. Two species have been documented in one region only: P. mariae in northeastern North America and P. marymargaretae in western North America. A combination of location, macromorphology, and spore size will usually differentiate the species of the complex.