Margarita Dueñas

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.

Fungal Planet description sheets: 154–213

Novel species of microfungi described in the present study include the following from South Africa: Camarosporium aloes, Phaeococcomyces aloes and Phoma aloes from Aloe, C. psoraleae, Diaporthe psoraleae and D. psoraleae-pinnatae from Psoralea, Colletotrichum euphorbiae from Euphorbia, Coniothyrium prosopidis and Peyronellaea prosopidis from Prosopis, Diaporthe cassines from Cassine, D. diospyricola from Diospyros, Diaporthe maytenicola from Maytenus, Harknessia proteae from Protea, Neofusicoccum ursorum and N. cryptoaustrale from Eucalyptus, Ochrocladosporium adansoniae from Adansonia, Pilidium pseudoconcavum from Greyia radlkoferi, Stagonospora pseudopaludosa from Phragmites and Toxicocladosporium ficiniae from Ficinia. Several species were also described from Thailand, namely: Chaetopsina pini and C. pinicola from Pinus spp., Myrmecridium thailandicum from reed litter, Passalora pseudotithoniae from Tithonia, Pallidocercospora ventilago from Ventilago, Pyricularia bothriochloae from Bothriochloa and Sphaerulina rhododendricola from Rhododendron. Novelties from Spain include Cladophialophora multiseptata, Knufia tsunedae and Pleuroascus rectipilus from soil and Cyphellophora catalaunica from river sediments. Species from the USA include Bipolaris drechsleri from Microstegium, Calonectria blephiliae from Blephilia, Kellermania macrospora (epitype) and K. pseudoyuccigena from Yucca. Three new species are described from Mexico, namely Neophaeosphaeria agaves and K. agaves from Agave and Phytophthora ipomoeae from Ipomoea. Other African species include Calonectria mossambicensis from Eucalyptus (Mozambique), Harzia cameroonensis from an unknown creeper (Cameroon), Mastigosporella anisophylleae from Anisophyllea (Zambia) and Teratosphaeria terminaliae from Terminalia (Zimbabwe). Species from Europe include Auxarthron longisporum from forest soil (Portugal), Discosia pseudoartocreas from Tilia (Austria), Paraconiothyrium polonense and P. lycopodinum from Lycopodium (Poland) and Stachybotrys oleronensis from Iris (France). Two species of Chrysosporium are described from Antarctica, namely C. magnasporum and C. oceanitesii. Finally, Licea xanthospora is described from Australia, Hypochnicium huinayensis from Chile and Custingophora blanchettei from Uruguay. Novel genera of Ascomycetes include Neomycosphaerella from Pseudopentameris macrantha (South Africa), and Paramycosphaerella from Brachystegia sp. (Zimbabwe). Novel hyphomycete genera include Pseudocatenomycopsis from Rothmannia (Zambia), Neopseudocercospora from Terminalia (Zambia) and Neodeightoniella from Phragmites (South Africa), while Dimorphiopsis from Brachystegia (Zambia) represents a novel coelomycetous genus. Furthermore, Alanphillipsia is introduced as a new genus in the Botryosphaeriaceae with four species, A. aloes, A. aloeigena and A. aloetica from Aloe spp. and A. euphorbiae from Euphorbia sp. (South Africa). A new combination is also proposed for Brachysporium torulosum (Deightoniella black tip of banana) as Corynespora torulosa. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Fungal Planet description sheets: 400–468

Novel species of fungi described in the present study include the following from Australia: Vermiculariopsiella eucalypti, Mulderomyces natalis (incl. Mulderomyces gen. nov.), Fusicladium paraamoenum, Neotrimmatostroma paraexcentricum, and Pseudophloeospora eucalyptorum on leaves of Eucalyptus spp., Anungitea grevilleae (on leaves of Grevillea sp.), Pyrenochaeta acaciae (on leaves of Acacia sp.), and Brunneocarpos banksiae (incl. Brunneocarpos gen. nov.) on cones of Banksia attenuata. Novel foliicolous taxa from South Africa include Neosulcatispora strelitziae (on Strelitzia nicolai), Colletotrichum ledebouriae (on Ledebouria floridunda), Cylindrosympodioides brabejum (incl. Cylindrosympodioides gen. nov.) on Brabejum stellatifolium, Sclerostagonospora ericae (on Erica sp.), Setophoma cyperi (on Cyperus sphaerocephala), and Phaeosphaeria breonadiae (on Breonadia microcephala). Novelties described from Robben Island (South Africa) include Wojnowiciella cissampeli and Diaporthe cissampeli (both on Cissampelos capensis), Phaeotheca salicorniae (on Salicornia meyeriana), Paracylindrocarpon aloicola (incl. Paracylindrocarpon gen. nov.) on Aloe sp., and Libertasomyces myopori (incl. Libertasomyces gen. nov.) on Myoporum serratum. Several novelties are recorded from La Réunion (France), namely Phaeosphaeriopsis agapanthi (on Agapanthus sp.), Roussoella solani (on Solanum mauritianum), Vermiculariopsiella acaciae (on Acacia heterophylla), Dothiorella acacicola (on Acacia mearnsii), Chalara clidemiae (on Clidemia hirta), Cytospora tibouchinae (on Tibouchina semidecandra), Diaporthe ocoteae (on Ocotea obtusata), Castanediella eucalypticola, Phaeophleospora eucalypticola and Fusicladium eucalypticola (on Eucalyptus robusta), Lareunionomyces syzygii (incl. Lareunionomyces gen. nov.) and Parawiesneriomyces syzygii (incl. Parawiesneriomyces gen. nov.) on leaves of Syzygium jambos. Novel taxa from the USA include Meristemomyces arctostaphylos (on Arctostaphylos patula), Ochroconis dracaenae (on Dracaena reflexa), Rasamsonia columbiensis (air of a hotel conference room), Paecilomyces tabacinus (on Nicotiana tabacum), Toxicocladosporium hominis (from human broncoalveolar lavage fluid), Nothophoma macrospora (from respiratory secretion of a patient with pneumonia), and Penidiellopsis radicularis (incl. Penidiellopsis gen. nov.) from a human nail. Novel taxa described from Malaysia include Prosopidicola albizziae (on Albizzia falcataria), Proxipyricularia asari (on Asarum sp.), Diaporthe passifloricola (on Passiflora foetida), Paramycoleptodiscus albizziae (incl. Paramycoleptodiscus gen. nov.) on Albizzia falcataria, and Malaysiasca phaii (incl. Malaysiasca gen. nov.) on Phaius reflexipetalus. Two species are newly described from human patients in the Czech Republic, namely Microascus longicollis (from toenails of patient with suspected onychomycosis), and Chrysosporium echinulatum (from sole skin of patient). Furthermore, Alternaria quercicola is described on leaves of Quercus brantii (Iran), Stemphylium beticola on leaves of Beta vulgaris (The Netherlands), Scleroderma capeverdeanum on soil (Cape Verde Islands), Scleroderma dunensis on soil, and Blastobotrys meliponae from bee honey (Brazil), Ganoderma mbrekobenum on angiosperms (Ghana), Geoglossum raitviirii and Entoloma kruticianum on soil (Russia), Priceomyces vitoshaensis on Pterostichus melas (Carabidae) (Bulgaria) is the only one for which the family is listed, Ganoderma ecuadoriense on decaying wood (Ecuador), Thyrostroma cornicola on Cornus officinalis (Korea), Cercophora vinosa on decorticated branch of Salix sp. (France), Coprinus pinetorum, Coprinus littoralis and Xerocomellus poederi on soil (Spain). Two new genera from Colombia include Helminthosporiella and Uwemyces on leaves of Elaeis oleifera. Two species are described from India, namely Russula intervenosa (ectomycorrhizal with Shorea robusta), and Crinipellis odorata (on bark of Mytragyna parviflora). Novelties from Thailand include Cyphellophora gamsii (on leaf litter), Pisolithus aureosericeus and Corynascus citrinus (on soil). Two species are newly described from Citrus in Italy, namely Dendryphiella paravinosa on Citrus sinensis, and Ramularia citricola on Citrus floridana. Morphological and culture characteristics along with ITS nrDNA barcodes are provided for all taxa.

Morphological and molecular studies of Hyphodermella in the Western Mediterranean area

The genus Hyphodermella was studied based on material from the western Mediterranean area (France, Italy, Spain, Portugal and Morocco) where the following three species have been recognized: H. corrugata (Fr.) J. Erikss. & Ryvarden, widely distributed, H. densa Melo & Hjortstam, only known from Portugal, and H. rosae (Bres.) Nakasone described from Italy. Twenty-one new ITS nrDNA sequences from these species, including the holotype collection of H. rosae and the paratype of H. densa, were aligned with one obtained from GenBank. The molecular results show that these collections are distributed in two highly supported monophyletic clades: one corresponds to H. corrugata, and the other one with H. densa and H. rosae collections. Morphological studies, including the type collections of the three taxa, show significant differences between the clades if we take into account the size of basidia and spores. The present study confirms H. corrugata as an independent species of H. rosae and H. densa, and that H. densa and H. rosae are conspecific; consequently, H. densa is a synonym of H. rosae. This last species is widely distributed in the Mediterranean area (France, Italy, Spain and Portugal) and as frequent as H. corrugata. Comments are offered on sequencing the barcode from types and well-annotated specimens.

A re-evaluation of Hypochnicium (Polyporales) based on morphological and molecular characters.

Hypochnicium is a genus of corticioid, wood-inhabiting fungi in the Polyporales with a worldwide distribution. The genus has been characterized by the nature of the spores; they are thick-walled, smooth or ornamented, and cyanophilous. Nine new ITS nrDNA sequences from species of this genus were aligned with 32 sequences from GenBank, and phylogenetic analyses were performed. Six clades were determined within the genus; one contains taxa with smooth spores, and the other three with ornamented spores. Hypochnicium versatum must be included in Gloeohypochnicium, and the new combination Gloeohypochnicium versatum is proposed. Two new species, Hypochnicium michelii from Spain and Hypochnicium guineensis from Equatorial Guinea, are described.

Diversity and richness of corticioid fungi (Basidiomycota) on Azores Islands: a preliminary survey

The diversity and species richness of corticioid fungi from three islands of the central group of the Azores Archipelago (Faial, Pico and Terceira) are analysed. The study covered 23 localities and found 88 species belonging to 44 genera, 73 being new to the Azores. Hyphodontia, Hyphoderma, Peniophora and Trechispora are the more significant genera and 36% of these genera are represented by one species only. Considering the available data, it is concluded that this biota shares 73% of its species with that of the East coast of North America, 83% with that of SW Europe (Spain and Portugal), 63% with that of the Canary Islands and 39% with that of Morocco.

Molecular analyses confirm Brevicellicium in Trechisporales.

The genus Brevicellicium encompasses wood-inhabiting corticioid fungi characterized by isodiametric subhymenial hyphae, short basidia, and smooth, often subangular spores with a distinct apiculus. Eight new LSU nrDNA sequences and 13 new ITS nrDNA of this genus, including the type species, were aligned with 47 and 42 accessions respectively of species of Trechisporales obtained from GenBank, and phylogenetic analyses were performed. The order Trechisporales was confirmed as a monophyletic group; the genera Porpomyces, Sistotremastrum, Subulicystidium and Trechispora form a highly supported clade where all Brevicellicium sequences are included. Our analyses also support that this genus belongs to Hydnodontaceae. A new species, Brevicellicium atlanticum from the Azores Archipelago, is described.

European species of Clavaria (Agaricales, Agaricomycetes) with dark basidiomata - a morphological and molecular study

Clavaria species with dark basidiomata occurring in Europe were analysed using morphological and molecular methods. Morphological analyses revealed four groups containing seven Clavaria species with dark basidiomata. Phylogenetic analysis of the LSU nrDNA region confirmed the separate positions of all seven Clavaria species within the genus. All sequences were grouped in four well-supported clades, mostly corresponding to defined morphological species. The results of the molecular study are inconsistent with the infrageneric classification of Clavaria based on the presence or absence of clamps on the bases of basidia and two widely accepted subgenera. Clavaria and Holocoryne appear to be polyphyletic. A new approach in species delimitation is presented: 1) C. asperulispora and C. atrofusca are two distinct species recognized by the shape of their spores, and the name C. neo-nigrita is a possible synonym of C. asperulispora; 2) species with clustered fragile basidiomata, C. fumosa and Clavaria cf. fuscoferruginea, which are almost identical in shape and size of spores differing only in the darker basidiomata of the latter, are phylogenetically unrelated; 3) Clavaria atrobadia is a dubious species, the name being most likely a synonym of C. fuscoferruginea; 4) two species with close morphological and phylogenetic affinity, C. atroumbrina and C. pullei, are distinguished based on the more oblong and narrower spores of the former. Comparison of European and North American material suggests the transatlantic nature of the distribution of C. asperulispora, C. atroumbrina and C. fumosa.

Gloeodontia xerophila (Aphyllophorales, Basidiomycota), a new species with corticioid basidioma from the Canary Islands.

Gloeodontia xerophila sp. nov. is described and illustrated from material collected on dead xerophyte debris in the Canary Islands. This species is characterized by the odontioid hymenophore with short aculei, up to 2 mm long, dimitic hyphal system and amyloid, subglobose and verrucose spores, 4–5 × 3–4 μm. The new taxon is compared with other species in the genus and a key to the species of Gloeodontia is provided.

Spelling out Jaapia species

Jaapia is a wood-saprobic genus of corticioid fungi for which two species have been recognized: J. argillacea Bres. and J. ochroleuca (Bres.) Nannf. & J. Erikss. Whereas the first one is easily recognized by its characteristic spores, the descriptions of the second indicated variable spores, which once led us to believe that J. ochroleuca could be a species complex rather than a single species. Eleven new ITS nrDNA sequences of J. ochroleuca were aligned with two obtained from GenBank and four of J. argillacea. The molecular results, parsimony analysis and KP2 distances clearly delimitate one highly supported Jaapia clade, with two subclades that correspond to the two described species. Morphological studies, including the holotype and isotype of J. ochroleuca, show significant differences between the clades concerning the size and shape of spores. The present study corroborates two species in this genus and also confirms that J. ochroleuca is a well-defined species in which spores show great morphological variability. Based on the Jaapia “species hypothesis”, the J. ochroleuca reference sequence has been selected. A comprehensive key to two Jaapia species is also provided.