Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov.

A new species of the yeast genus Blastobotrys was discovered during a worldwide survey of culturable xerophilic fungi in house dust. Several culture-dependent and independent studies from around the world detected the same species from a wide range of substrates including indoor air, cave wall paintings, bats, mummies, and the iconic self-portrait of Leonardo da Vinci from ca 1512. However, none of these studies identified their strains, clones, or OTUs as Blastobotrys. We introduce the new species as Blastobotrys davincii f.a., sp. nov. (holotype CBS H-24879) and delineate it from other species using morphological, phylogenetic, and physiological characters. The new species of asexually (anamorphic) budding yeast is classified in Trichomonascaceae and forms a clade along with its associated sexual state genus Trichomonascus. Despite the decade-old requirement to use a single generic name for fungi, both names are still used. Selection of the preferred name awaits a formal nomenclatural proposal. We present arguments for adopting Blastobotrys over Trichomonascus and introduce four new combinations as Blastobotrys allociferrii (≡ Candida allociferrii), B. fungorum (≡ Sporothrix fungorum), B. mucifer (≡ Candida mucifera), and Blastobotrys vanleenenianus (≡ Trichomonascus vanleenenianus). We provide a nomenclatural review and an accepted species list for the 37 accepted species in the Blastobotrys/Trichomonascus clade. Finally, we discuss the identity of the DNA clones detected on the da Vinci portrait, and the importance of using appropriate media to isolate xerophilic or halophilic fungi.

Assessing Performance of Spore Samplers in Monitoring Aeromycobiota and Fungal Plant Pathogen Diversity in Canada.

Spore samplers are widely used in pathogen surveillance but not so much for monitoring the composition of aeromycobiota. In Canada, a nationwide spore-sampling network (AeroNet) was established as a pilot project to assess fungal community composition in air and rain samples collected using three different spore samplers in the summers of 2010 and 2011. Metabarcodes of the internal transcribed spacer (ITS) were exhaustively characterized for three of the network sites, in British Columbia (BC), Québec (QC), and Prince Edward Island (PEI), to compare performance of the samplers. Sampler type accounted for ca. 20% of the total explainable variance in aeromycobiota compositional heterogeneity, with air samplers recovering more Ascomycota and rain samplers recovering more Basidiomycota. Spore samplers showed different abilities to collect 27 fungal genera that are plant pathogens. For instance, Cladosporium spp., Drechslera spp., and Entyloma spp. were collected mainly by air samplers, while Fusarium spp., Microdochium spp., and Ustilago spp. were recovered more frequently with rain samplers. The diversity and abundance of some fungi were significantly affected by sampling location and time (e.g., Alternaria and Bipolaris) and weather conditions (e.g., Mycocentrospora and Leptosphaeria), and depended on using ITS1 or ITS2 as the barcoding region (e.g., Epicoccum and Botrytis). The observation that Canada's aeromycobiota diversity correlates with cooler, wetter conditions and northward wind requires support from more long-term data sets. Our vision of the AeroNet network, combined with high-throughput sequencing (HTS) and well-designed sampling strategies, may contribute significantly to a national biovigilance network for protecting plants of agricultural and economic importance in Canada.IMPORTANCE The current study compared the performance of spore samplers for collecting broad-spectrum air- and rain-borne fungal pathogens using a metabarcoding approach. The results provided a thorough characterization of the aeromycobiota in the coastal regions of Canada in relation to the influence of climatic factors. This study lays the methodological basis to eventually develop knowledge-based guidance on pest surveillance by assisting in the selection of appropriate spore samplers.

Sexual and asexual states of some endophytic Phialocephala species of Picea.

Unidentified DNA sequences in isolation-based or culture-free studies of conifer endophytes are a persistent problem that requires a field approach to resolve. An investigation of foliar endophytes of Picea glauca, P. mariana, P. rubens and Pinus strobus in eastern Canada, using a combined field, morphological, cultural and DNA sequencing approach, resulted in the frequent isolation of Phialocephala spp. and the first verified discovery of their mollisia-like sexual states in the field. Phialocephala scopiformis and Ph. piceae were the most frequent species isolated as endophytes from healthy conifer needles. Corresponding Mollisia or mollisioid sexual states for Ph. scopiformis, Ph. piceae and several undescribed species in a clade containing Ph. dimorphospora were collected in the sampling area and characterized by analysis of the nuc internal transcribed spacer rDNA (ITS) and gene for the largest subunit of RNA polymerase II (RPB1) loci. Four novel species and one new combination in a clade containing Ph. dimorphospora, the type of Phialocephala, are presented, accompanied by descriptions of apothecia and previously undocumented synanamorphs. An epitype culture and corresponding reference sequences for Phialocephala dimorphospora are proposed. The resulting ITS barcodes linked with robust taxonomic species concepts are an important resource for future research on forest ecosystems and endophytes.

Xerotolerant fungi in house dust: taxonomy of Spiromastix, Pseudospiromastix and Sigleria gen. nov. in Spiromastigaceae (Onygenales, Eurotiomycetes).

During a global investigation of fungi in house dust, we isolated six novel arthroconidial fungi. Phylogenies from combined analysis of nuc rDNA 18S, 28S and internal transcribed spacers sequences demonstrated that these fungi and two species preserved in culture collections represent undescribed species of Spiromastigaceae, Onygenales. Seven of the eight species lacked sexual states and only characters of asexual states and growth rates on different media could be used to characterize them. The eighth species produced ascomata only on water agar. We introduce six new species and one new combination in Spiromastix and validate the recently proposed family Spiromastigaceae, genus Pseudospiromastix and combination Ps. tentaculata. The new genus Sigleria is proposed for two new species that differ from Spiromastix by conidiophore branching patterns, slower growth and a limited ability to utilize nitrate as a sole N source. A key to the three genera of Spiromastigaceae, Spiromastix, Pseudospiromastix and Sigleria, is provided. Phylogenetic analyses support the placement of Spiromastigaceae within Onygenales.

Product ion filtering with rapid polarity switching for the detection of all fumonisins and AAL-toxins.

RATIONALE: Fumonisins and AAL-toxins are structurally similar mycotoxins that contaminate agricultural crops and foodstuffs. Traditional analytical screening methods are designed to target the known compounds for which standards are available but there is clear evidence that many other derivatives exist and could be toxic. A fast, semi-targeted method for the detection of all known fumonisins, AAL-toxins and related emerging toxins is required. METHODS: Strains of Fusarium verticillioides, Alternaria arborescens and Aspergillus welwitschiae were grown on their associated crops (maize, tomatoes, and grapes, respectively). Extracts were first analyzed in negative mode using product ion filtering to detect the tricarballylic ester product ion that is common to fumonisins and AAL-toxins (m/z 157.0142). During the same liquid chromatography (LC) run, rapid polarity switching was then used to collect positive mode tandem mass spectrometric (MS(2) ) data for characterization of the detected compounds. RESULTS: Fumonisin B1 , B2 , B3 and B4 were detected on Fusarium contaminated maize, AAL-toxins TA, TB, TD, TE were detected on Alternaria inoculated tomatoes and fumonisin B2 , B4 and B6 on Aspergillus contaminated grapes. Additionally, over 100 structurally related compounds possessing a tricarballylic ester were detected from the mould inoculated plant material. These included a hydroxyl-FB1 from F. verticillioides inoculated maize, keto derivatives of AAL-toxins from A. arborescens inoculated tomatoes, and two previously unreported classes of non-aminated fumonisins from Asp. welwitschiae contaminated grapes. CONCLUSIONS: A semi-targeted method for the detection of all fumonisins and AAL-toxins in foodstuffs was developed. The use of the distinctive tricarballylic ester product anion for detection combined with rapid polarity switching and positive mode MS(2) is an effective strategy for differentiating between known isomers such as FB1 and FB6 . This analytical tool is also effective for the identification of new compounds as evident from the discoveries of the previously unreported hydroxyl-FB1 , keto-AAL-toxins, and the two new families of non-aminated fumonisins.

Identification of six new Alternaria sulfoconjugated metabolites by high-resolution neutral loss filtering.

RATIONALE: Many species of Alternaria damage important agricultural crops, including small grains and tomatoes. These fungi can produce a variety of secondary metabolites, some of which are toxic to humans and animals. Interest in screening for conjugated or 'modified' mycotoxins has increased because of their tendency to evade traditional analytical screening methods. Two sulfoconjugated Alternaria toxins have been reported and the potential exists for many more. METHODS: One hundred and forty-eight Canadian strains of Alternaria spp., about half of them isolated from grain, were grown on Potato Dextrose Agar in Petri dishes for 7 days. Plugs of each strain were removed, extracted and screened by a rapid liquid chromatography (LC)/data-dependent tandem mass spectrometry (MS(2)) method in negative electrospray ionization mode. Data generated on an Orbitrap Q-Exactive mass spectrometer was processed by post-acquisition neutral loss filtering (NLF). Seven isolates that produced sulfoconjugates of known Alternaria toxins were selected for growth on three additional types of fermentation media. RESULTS: Collision-induced dissociation of sulfoconjugated ions displayed a distinctive neutral loss of SO3 (79.957 Da) that was detected in the MS(2) datasets using post-acquisition NLF. A total of 108 of the 148 isolates screened produced sulfoconjugated metabolites on agar plates. Analysis of the seven isolates grown in liquid culture, on rice and Cheerios, led to the discovery of six new, two previously reported and 30 unidentified sulfoconjugated compounds. CONCLUSIONS: NLF of HRMS(2) data from an Orbitrap Q-Exactive is a powerful tool for the rapid discovery of sulfoconjugated fungal metabolites. This technique could also be applied to the detection of other important conjugated mycotoxins such as glucosides. The majority of the Canadian isolates of Alternaria spp. studied produced sulfoconjugated metabolites, some of which had no known 'free' Alternaria precursor metabolite, indicating that they are possibly new metabolites. The advantage of sulfoconjugation to Alternaria spp. is unknown, and warrants further study into the mechanisms behind the sulfur assimilatory pathways.

A century later: rediscovery, culturing and phylogenetic analysis of Diploöspora rosea, a rare onygenalean hyphomycete.

Nearly 100 years after its first discovery, Diploöspora rosea was detected on biologically damaged parchment paper in Rome, Italy and isolated from house dust collected in Micronesia. The isolation of this culture permitted morphological study of colony characters, conidium and conidiophore development, and phylogenetic investigations using sequences of nuc 18S rDNA, internal transcribed spacers, and 28S rDNA. The results indicate that D. rosea is an onygenalean fungus, of uncertain taxonomic position, basal or sister to the Gymnoascaceae. Based on observations of the parchments using SEM-Energy Dispersive Spectroscopy, we speculate that the fungus occurs in archival and domestic environments subject to periodic wetting. Its ability to grow on all low water activity media used in the study, including malt extract agar amended with 60% sucrose, confirms its xerophilic nature.

Escovopsis trichodermoides sp. nov., isolated from a nest of the lower attine ant Mycocepurus goeldii.

Currently, five species are formally described in Escovopsis, a specialized mycoparasitic genus of fungus gardens of attine ants (Hymenoptera: Formicidae: tribe Attini). Four species were isolated from leaf-cutting ants in Brazil, including Escovopsis moelleri and Escovopsis microspora from nests of Acromyrmex subterraneus molestans, Escovopsis weberi from a nest of Atta sp. and Escovopsis lentecrescens from a nest of Acromyrmex subterraneus subterraneus. The fifth species, Escovopsis aspergilloides was isolated from a nest of the higher attine ant Trachymyrmex ruthae from Trinidad. Here, we describe a new species, Escovopsis trichodermoides isolated from a fungus garden of the lower attine ant Mycocepurus goeldii, which differs from the five other species by highly branched, trichoderma-like conidiophores lacking swollen vesicles, with reduced conidiogenous cells and distinctive conidia morphology. Phylogenetic analyses based on partial tef1 gene sequences support the distinctiveness of this species. A portion of the internal transcribed spacers of the nuclear rDNA was sequenced to serve as a DNA barcode. Future molecular and morphological studies in this group of fungi will certainly unravel the taxonomic diversity of Escovopsis associated with fungus-growing ants.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

Diversity of Penicillium section Citrina within the fynbos biome of South Africa, including a new species from a Protea repens infructescence.

During a survey of the fynbos biome in the Western Cape of South Africa, 61 Penicillium species were isolated and nine belong to Penicillium section Citrina. Based on morphology and multigene phylogenies, section Citrina species were identified as P. cairnsense, P. citrinum, P. pancosmium, P. pasqualense, P. sanguifluum, P. sizovae, P. sumatrense and P. ubiquetum. One of the species displayed unique phenotypic characters and DNA sequences and is described here as P. sucrivorum. Multigene phylogenies consistently resolved the new species in a clade with P. aurantiacobrunneum, P. cairnsense, P. miczynksii, P. neomiczynskii and P. quebecense. However, ITS, ß-tubulin and calmodulin gene sequences are unique for P. sucrivorum and growth rates on various media, the ability to grow at 30 C, a positive Ehrlich reaction and the absence of sclerotia on all media examined, distinguish P. sucrivorum from all of its close relatives.

Identification and Detection of Fusarium striatum as a New Record of Pathogen to Greenhouse Tomato in Northeastern America.

Recently, a new disease was reported on greenhouse tomato plants in both Quebec, Canada and Maine, United States. Symptomatic plants bore brown lesions at graft points and pruning sites, resulting in expanding cankers with clearly delineated margins. Diseased plants eventually wilted and died within a few weeks following the appearance of the first symptoms. The symptoms are reminiscent of infection by Fusarium oxysporum f. sp. radicis-lycopersici, with the notable difference of a discoloration of the pith area rather than the vascular tissues. A homothallic Fusarium sp. was consistently recovered from these lesions. Sequencing of the internal transcribed spacer and the partial translation elongation factor 1-α gene identified the species as F. striatum. Pathogenicity tests with F. striatum isolates from diseased tissues reproduced disease symptoms in tomato similar to those observed on tomato plants in the greenhouses. Specific detection of F. striatum from mycelia and diseased and disease-free plant tissues was achieved by developing a polymerase chain reaction-based test. These results establish, for the first time, that the species F. striatum is the cause of crown and stem rot affecting tomato in North America. In addition F. striatum was detected from all sampled tissues of plants delivered by the nursery common to both growers, suggesting that the transplants would be the source of the inoculum.

Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics.

Fungi are ubiquitous components of indoor human environments, where most contact between humans and microbes occurs. The majority of these organisms apparently play a neutral role, but some are detrimental to human lifestyles and health. Recent studies that used culture-independent sampling methods demonstrated a high diversity of indoor fungi distinct from that of outdoor environments. Others have shown temporal fluctuations of fungal assemblages in human environments and modest correlations with human activity, but global-scale patterns have not been examined, despite the manifest significance of biogeography in other microbial systems. Here we present a global survey of fungi from indoor environments (n = 72), using both taxonomic and phylogeny-informative molecular markers to determine whether global or local indoor factors determine indoor fungal composition. Contrary to common ecological patterns, we show that fungal diversity is significantly higher in temperate zones than in the tropics, with distance from the equator being the best predictor of phylogenetic community similarity. Fungal composition is significantly auto-correlated at the national and hemispheric spatial scales. Remarkably, building function has no significant effect on indoor fungal composition, despite stark contrasts between architecture and materials of some buildings in close proximity. Distribution of individual taxa is significantly range- and latitude-limited compared with a null model of randomized distribution. Our results suggest that factors driving fungal composition are primarily global rather than mediated by building design or function.

Basidioascus and Geminibasidium: a new lineage of heat-resistant and xerotolerant basidiomycetes.

Using a heat-treatment method, two genera of heat-resistant and xerotolerant basidiomycetes were isolated from soil samples. These two genera, Basidioascus and Geminibasidium gen. nov., are morphologically similar and phylogenetically related. The genus Basidioascus originally was described as an ascomycete, but the structures originally interpreted as single-spored asci appear to represent basidiospores. Morphologically both genera are characterized by the lack of a fruiting body, conspicuously granular and deciduous basidia with a unique basal lateral projection and apparently double-walled basidiospores. The basidia, rather than the basidiospores, are forcibly discharged in Basidioascus species but not in Geminibasidium species. In Geminibasidium species a putative basidium arises from a primary cell. These are novel forms of basidia ontogenesis previously unseen in basidiomycetes. The rDNA (SSU + 5.8S + LSU) Bayesian phylogenetic analysis suggests that these fungi are distantly related to Wallemia, another xerotolerant basidiomycete genus commonly found in indoor air dust, dried foods and natural hypersaline environments. Given the physiological similarity and phylogenetic relationships, Basidioascus and Geminibasidium are classified in a new order, Geminibasidiales, and are taxonomically assigned to the class Wallemiomycetes. Based on morphological observations and molecular phylogeny of the internal transcribed spacer (ITS), two species of Basidioascus (B. undulatus, B. magus sp. nov.) and two species of Geminibasidium (G. donsium sp. nov., G. hirsutum sp. nov.) are described. A key to these species is provided using micromorphological and cultural characters.

Cirrosporium novae-zelandiae, an enigmatic coelomycete with meristem arthroconidia, with ancestors in the Eurotiomycetes.

A culture of Cirrosporium novae-zelandiae, the type species of a distinctive, monotypic coelomycete genus, was isolated from a specimen collected near the holotype locality in New Zealand. Light microscopic and environmental scanning electron microscopic observations confirm the details of the unusual meristem arthric conidium ontogeny presented in the protolog. For phylogenetic analysis, a dataset of 122 species representing nine classes of euascomycetes was assembled including sequences from nuclear small and large subunits (nc18S, nc28S) and mitochondrial small subunit (mr16S) ribosomal RNA and the largest and second largest subunits of RNA polymerase II (RPB1, RPB2). A five-gene phylogeny suggests that the fungus is phylogenetically related to the Eurotiomycetes. It sits alone on a long branch as a sister to the Mycocaliciales of the Mycocaliciomycetidae. Cirrosporium exhibits several morphological characters similar to those of members of the Mycocaliciales; however, the paucity of known anamorphs in this order does not offer any further clarification on possible relationships. It is clear that the rare and broadly distributed meristem arthric ontogenetic pattern is polyphyletic, occurring in widely separate groups of anamorphs of both the Ascomycota and Basidiomycota.

Phylogenetic classification of Pleurothecium and Pleurotheciella gen. nov. and its dactylaria-like anamorph (Sordariomycetes) based on nuclear ribosomal and protein-coding genes.

Two strains of an unidentified perithecial ascomycete with a dactylaria-like anamorph and another morphologically similar strain of a dactylaria-like fungus were collected on decaying wood submerged in freshwater. To study their phylogenetic relationships we (i) combined sequence data from the nuclear small and large subunits ribosomal DNA (nc18S and nc28S) and the second largest subunit of RNA polymerase II (RPB2) for a multigene phylogenetic analysis and (ii) used sequences of the internal transcribed spacer region (ITS) of the rRNA operon for a species-level analysis. The new genus Pleurotheciella is described for two new species, Pla. rivularia and Pla. centenaria, with nonstromatic perithecia, unitunicate asci, persistent paraphyses and hyaline, septate ascospores and dactylaria-like anamorphs characterized by holoblastic, denticulate conidiogenesis, subhyaline conidiophores and hyaline, septate conidia. Based on morphological and molecular data, Pleurotheciella is closely related to the genera Pleurothecium and Sterigmatobotrys. A key to the three genera and the known species is provided. In the three-gene inferred phylogeny, these genera grouped as a sister clade to the Savoryellales within a robust clade of uncertain higher rank affiliation. Phylogenetic study of the 12 strains that represent Pleurothecium recurvatum revealed four that grouped apart from the core of the species. Two of these strains, which form a monophyletic well supported clade in both phylogenies and share similar morphological characteristics, are described as a new species, Pleurothecium semifecundum.

Fusarium abutilonis and F. guadeloupense, two novel species in the Fusarium buharicum clade supported by multilocus molecular phylogenetic analyses.

This study was conducted to elucidate evolutionary relationships and species diversity within the Fusarium buharicum species complex (FBSC). We also evaluate the potential of these species to produce mycotoxins and other bioactive secondary metabolites. Maximum likelihood and maximum parsimony analyses of sequences from portions of four marker loci (ITS rDNA, TEF1, RPB1, and RPB2) and the combined 4495 bp data set support recognition of seven genealogically exclusive species within the FBSC. Two of the three newly discovered species are formally described as F. abutilonis and F. guadeloupense based on concordance of gene genealogies and morphological data. Fusarium abutilonis induces leaf, stem, and root lesions on several weedy Malvaceae (Abution theophrasti, Anoda cristata, Sida spinosa) and a fabaceous host (Senna obtusifolia) in North America and also was recovered from soil in New Caledonia. Fusarium abutilonis, together with its unnamed sister, Fusarium sp. ex common marsh mallow (Hibiscus moscheutos) from Washington state, and F. buharicum pathogenic to cotton and kenaf in Russia and Iran, respectively, were strongly supported as a clade of malvaceous pathogens. The four other species of the FBSC are not known to be phytopathogenic; however, F. guadeloupense was isolated from human blood in Texas and soil in Guadeloupe. The former isolate is unique because it represents the only known case of a fusarial infection disseminated hematogenously by a species lacking microconidia and the only documented fusariosis caused by a member of the FBSC. Whole genome sequence data and extracts of cracked maize kernel cultures were analyzed to assess the potential of FBSC isolates to produce mycotoxins, pigments, and phytohormones.

Identification of N,N',N″-triacetylfusarinine C as a key metabolite for root rot disease virulence in American ginseng.

BACKGROUND: It is estimated that 20-30% of ginseng crops in Canada are lost to root rot each harvest. This disease is commonly caused by fungal infection with Ilyonectria, previously known as Cylindrocarpon. Previous reports have linked the virulence of fungal disease to the production of siderophores, a class of small-molecule iron chelators. However, these siderophores have not been identified in Ilyonectria. METHODS: High-resolution LC-MS/MS was used to screen Ilyonectria and Cylindrocarpon strain extracts for secondary metabolite production. These strains were also tested for their ability to cause root rot in American ginseng and categorized as virulent or avirulent. The differences in detected metabolites between the virulent and avirulent strains were compared with a focus on siderophores. RESULTS: For the first time, a siderophore N,N',N″-triacetylfusarinine C (TAFC) has been identified in Ilyonectria, and it appears to be linked to disease virulence. Siderophore production was suppressed as the concentration of iron increased, which is in agreement with previous reports. CONCLUSION: The identification of the siderophore produced by Ilyonectria gives us further insight into the root rot disease that heavily affects ginseng crop yields. This research identifies a molecular pathway previously unknown for ginseng root rot and could lead to new disease treatment options.

Competing sexual-asexual generic names in Agaricomycotina (Basidiomycota) with recommendations for use.

With the change to one scientific name for fungal taxa, generic names typified by species with sexual or asexual morph types are being evaluated to determine which names represent the same genus and thus compete for use. In this paper generic names of the Agaricomycotina (Basidiomycota) were evaluated to determine synonymy based on their type. Forty-seven sets of sexually and asexually typified names were determined to be congeneric and recommendations are made for which generic name to use. In most cases the principle of priority is followed. However, 16 generic names are recommended for use that do not have priority and thus need to be protected: Aleurocystis over Matula; Armillaria over Acurtis and Rhizomorpha; Asterophora over Ugola; Botryobasidium over Acladium, Allescheriella, Alysidium, Haplotrichum, Physospora, and Sporocephalium; Coprinellus over Ozonium; Coprinopsis over Rhacophyllus; Dendrocollybia over Sclerostilbum and Tilachlidiopsis; Diacanthodes over Bornetina; Echinoporia over Echinodia; Neolentinus over Digitellus; Postia over Ptychogaster; Riopa over Sporotrichum; Scytinostroma over Artocreas, Michenera, and Stereofomes; Tulasnella over Hormomyces; Typhula over Sclerotium; and Wolfiporia over Gemmularia and Pachyma. Nine species names are proposed for protection: Botryobasidium aureum, B. conspersum, B. croceum, B. simile, Pellicularia lembosporum (syn. B. lembosporum), Phanerochaete chrysosporium, Polyporus metamorphosus (syn. Riopa metamorphosa), Polyporus mylittae (syn. Laccocephalum mylittae), and Polyporus ptychogaster (syn. Postia ptychogaster). Two families are proposed for protection: Psathyrellaceae and Typhulaceae. Three new species names and 30 new combinations are established, and one lectotype is designated.

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

Pyrosequencing technologies have revolutionized how we describe and compare complex microbial communities. In 454 pyrosequencing data sets, the abundance of reads pertaining to taxa or phylotypes is commonly interpreted as a measure of genic or taxon abundance, useful for quantitative comparisons of community similarity. Potentially systematic biases inherent in sample processing, amplification and sequencing, however, may alter read abundance and reduce the utility of quantitative metrics. Here, we examine the relationship between read abundance and biological abundance in a sample of house dust spiked with known quantities and identities of fungi along a dilution gradient. Our results show one order of magnitude differences in read abundance among species. Precision of quantification within species along the dilution gradient varied from R(2) of 0.96-0.54. Read-quality based processing stringency profoundly affected the abundance of one species containing long homopolymers in a read orientation-biased manner. Order-level composition of background environmental fungal communities determined from pyrosequencing data was comparable with that derived from cloning and Sanger sequencing and was not biased by read orientation. We conclude that read abundance is approximately quantitative within species, but between-species comparisons can be biased by innate sequence structure. Our results showed a trade off between sequence quality stringency and quantification. Careful consideration of sequence processing methods and community analyses are warranted when testing hypotheses using read abundance data.