Evolutionary relationships of members of the genera Taphrina, Protomyces, Schizosaccharomyces, and related taxa within the archiascomycetes: Integrated analysis of genotypic and phenotypic characters

Novakomyces olei sp. nov., the First Member of a Novel Taphrinomycotina Lineage

Taphrinomycotina is the smallest subphylum of the phylum Ascomycota. It is an assemblage of distantly related early diverging lineages of the phylum, comprising organisms with divergent morphology and ecology; however, phylogenomic analyses support its monophyly. In this study, we report the isolation of a yeast strain, which could not be assigned to any of the currently recognised five classes of Taphrinomycotina. The strain of the novel budding species was recovered from extra virgin olive oil and characterised phenotypically by standard methods. The ultrastructure of the cell wall was investigated by transmission electron microscopy. Comparisons of barcoding DNA sequences indicated that the investigated strain is not closely related to any known organism. Tentative phylogenetic placement was achieved by maximum-likelihood analysis of the D1/D2 domain of the nuclear LSU rRNA gene. The genome of the investigated strain was sequenced, assembled, and annotated. Phylogenomic analyses placed it next to the fission Schizosaccharomyces species. To accommodate the novel species, Novakomyces olei, a novel genus Novakomyces, a novel family Novakomycetaceae, a novel order Novakomycetales, and a novel class Novakomycetes is proposed as well. Functional analysis of genes missing in N. olei in comparison to Schizosaccharomyces pombe revealed that they are biased towards biosynthesis of complex organic molecules, regulation of mRNA, and the electron transport chain. Correlating the genome content and physiology among species of Taphrinomycotina revealed some discordance between pheno- and genotype. N. olei produced ascospores in axenic culture preceded by conjugation between two cells. We confirmed that N. olei is a primary homothallic species lacking genes for different mating types.

Kazachstania siamensis sp. nov., an ascomycetous yeast species from forest soil in Thailand

Two strains (S-34T and S-35) of a novel ascomycetous yeast species belonging to the genus Kazachstania were isolated from soil from a mixed deciduous forest in Amphoe Wang Nam Khiao, Nakhon Ratchasima Province, Thailand. The D1/D2 domains of the large-subunit rDNA sequences of the two strains were identical and also indicated a close relationship with respect to Kazachstania aquatica, Kazachstania unispora, Kazachstania aerobia, Kazachstania servazzii and Kazachstania solicola. The most closely related species, K. aquatica, has 14 nucleotide substitutions and three gaps in 566 nt. The phenotypic characteristics of the two strains were typical of those of members of the genus Kazachstania. These characteristics include the formation of a single globose ascospore in an unconjugated and persistent ascus, multilateral budding, the absence of arthrospores and ballistospores, the fermentation of glucose, the inability to assimilate nitrate, negative diazonium blue B and urease reactions, and the presence of ubiquinone Q-6. The novel strains can be distinguished from K. aquatica on the basis of a number of phenotypic characteristics and represent a novel species in the genus Kazachstania, for which the name Kazachstania siamensis sp. nov. is proposed. The type strain is S-34T (=CBS 10361T=NBRC 101968T=BCC 21230T).

Pneumocystis and Trypanosoma cruzi: Nomenclature and Typifications

Published phylogenetic reclassifications of Pneumocystis as a fungus resulted in a nomenclatural shift from the Zoological Code to the International Code of Botanical Nomenclature. The same may be true for all microsporidians and sundry other organisms. This resulted in the invalidation of names and subsequently precipitated changes to the botanical code to accommodate Pneumocystis and microsporidian names. The repercussions following application of the 2005 Vienna Code to Pneumocystis nomenclature are detailed. Validity of the name for the human pathogen, Pneumocystis jirovecii, is re-established from its 1976 publication under the Zoological Code, contrary to interpretation of validity under earlier botanical codes. Pneumocystis jirovecii is lectotypified and epitypified. The rat parasite, Pneumocystis carinii, is neotypified, separating it from Pneumocystis wakefieldiae. The original 1909 description of Trypanosoma cruzi, type species for Schizotrypanum, and causal agent of Chagas' disease, included parts of the life cycle of Pneumocystis. Trypanosoma cruzi is neotypified by the true Trypanosoma elements, thereby completing the nomenclatural separation from Pneumocystis and ensuring that Schizotrypanum is not applicable to Pneumocystis as an earlier name. The neotypes for P. carinii and T. cruzi represent the strains currently being investigated by their two respective genome projects. They were selected in light of their medical importance, physiological characterizations, and absence of lectotypifiable materials. The classification and nomenclature of Pneumocystis is reviewed and guidelines given for the publication of new species.

Tetrapisispora namnaonensis sp. nov., a novel ascomycetous yeast species isolated from forest soil of Nam Nao National Park, Thailand

Twenty-one strains of a novel ascomycetous yeast species were isolated from soil collected in three kinds of natural forest, namely a dry dipterocarp forest, a mixed deciduous forest and a pine forest, in Nam Nao National Park, Phetchabun province, Thailand. The strains formed asci containing one to four ovoid to reniform ascospores, assimilated glucose, galactose and glycerol, fermented glucose and galactose vigorously and contained ubiquinone Q-6, indicating that they belonged to the genus Tetrapisispora. A comparative analysis of the small subunit rDNA (SSU rDNA) and the D1/D2 domain of the large subunit rDNA (LSU rDNA) of all available sequences for ascomycetous yeasts confirmed that the strains were phylogenetically related to the genus Tetrapisispora. All strains had identical nucleotide sequences in the D1/D2 domain of the LSU rDNA and differed from the nearest species, Tetrapisispora arboricola IFO 10925T, by 6·4 % nucleotide substitutions. The strains differed from Tetrapisispora arboricola by the ability to assimilate d-gluconic acid, the inability to grow on 50 % glucose medium, the nuclear DNA base composition and deliquescent asci. The strains were differentiated from the other four species of Tetrapisispora on the basis of trehalose assimilation, the ability to grow on 50 % glucose or 10 % NaCl plus 5 % glucose, vitamin requirement, the nuclear DNA base composition and the type of ascus. Based on the characteristics mentioned above, the strains are recognized as a single novel species of the genus Tetrapisispora and the name Tetrapisispora namnaonensis sp. nov. is proposed. The type strain is TN1-01T (=TISTR 5828T=JCM 12664T=CBS 10093T).

Taxonomy and phylogeny of the xerophilic genus Wallemia (Wallemiomycetes and Wallemiales, cl. et ord. nov.)

The genus Wallemia comprises xerophilic species. Based on parenthesome ultrastructure it has been linked to the Filobasidiales (basidiomycetes). Species show a unique type of conidiogenesis, including basauxic development of fertile hyphae, segregation of conidial units more or less basipetally, and disarticulation of conidial units into mostly four arthrospore-like conidia. Wallemia is known from air, soil, dried food (causing spoilage), and salt. It can be isolated from hypersaline water of man-made salterns on different continents. Based on analyses of the nuclear small subunit ribosomal DNA (SSU rDNA) Wallemia has been placed into a highly supported clade together with Ustilaginomycetes and Hymenomycetes (Basidiomycota). Within this clade, it possesses an isolated position distantly related to the Filobasidiales and was characterized by numerous nucleotide substitutions not shared by any other fungus. Tests on xerotolerance indicated that Wallemia presents one of the most xerophilic fungal taxa. Xerotolerance is otherwise rare in the Basidiomycota. To acknowledge its unique morphology, evolution, and xerotolerance, a new basidiomycetous class Wallemiomycetes covering an order Wallemiales, is proposed. Based on differences in conidial size, xerotolerance, and sequence data of the rDNA internal transcribed spacer regions (ITS rDNA), at least three Wallemia species are segregated, identified as Wallemia ichthyophaga, Wallemia sebi, and Torula epizoa var. muriae, for which the combination Wallemia muriae is proposed. The three species are neotypified. Wallemia ichthyophaga differs from W. sebi and W. muriae in numerous nucleotides of the SSU and ITS rDNA. This high variation within Wallemia indicates existence of at least two cryptic genera not distinguishable by morphological characters.

Characterisation and classification of phylloplane yeasts from Portugal related to the genus Taphrina and description of five novel Lalaria species

Taphrina Fries is a genus of dimorphic ascomycetes comprising more than 90 species distinguished by the specific infections they produce on different vascular plants. Their filamentous states are restricted to parasitised plant tissue whereas the yeast states are saprobic and can be grown on artificial media. The latter coincide with the anamorphic phases and have been given separate nomenclatural status by the erection of the genus Lalaria R.T. Moore. In its original circumscription Lalaria included only 23 yeast states of known species of Taphrina and its creation was then redundant. Here we describe five novel species in the genus Lalaria to accommodate a total of 44 yeast isolates obtained mainly from leaf surfaces (phylloplane) of different plants in Portugal: Lalaria arrabidae sp. nov. (one strain), L. carpini sp. nov. (one strain), L. inositophila sp. nov. (37 strains), L. kurtzmanii sp. nov. (one strain) and L. veronaerambellii sp. nov. (four strains). L. inositophila was notable for its widespread occurrence since it was recovered during two consecutive years from the leaves of miscellaneous plant species. In the absence of sexual states and of unequivocal associations to particular host plants, the taxonomic relationship of the novel species to the yeast states of Taphrina available from culture collections was verified by the comparative analysis of physiological and molecular characteristics. The latter included PCR fingerprinting using single primers for microsatellite regions, sequencing of the 5' end of the 26S rRNA (LSU) gene (D1/D2 domains) and of the ITS1 and ITS2 rDNA spacer regions, and DNA-DNA hybridisation experiments. An emended description of the genus Lalaria is provided.

Morphology and ultrastructure of Neolecta species

Several independent molecular phylogenetic analyses have indicated that the genus Neolecta has a unique position within the Ascomycota. It is the only taxon outside the core-group of filamentous, ascoma-forming ascomycetes that also has the ability to form ascomata. Light and electron microscope studies indicate that hymenial structure and development in Neolecta spp. are unique. Ascogenous hyphae in N. vitellina branched repeatedly and successively to produce asci. Non-ascogenous hyphae were multinucleate, often with nuclei in pairs. Nuclear pairing was particularily prominent in the ascogenous hyphae. A basal septum delimited the dikaryotic ascus. Ascosporogenesis was initiated by nuclear fusion followed by a meiotic and mitotic division to form eight nuclei. The ascus apex was thin with an annular subapical thickening. Ascospores were forcibly released through a 'split' in the ascus apex. Woronin bodies were frequently associated with hyphal septa. Attempts to culture N. vitellina and to obtain molecular information from the type species, N. flarovirescens, were unsuccessful. However, N. flavovirescens showed several microscopic characters that indicated close relationships with the two other species in the genus, N. vitellina and N. irregularis. The position of Neolecta spp. within the Ascomycota is discussed.

Three new combinations from the Cryptococcus laurentii complex: Cryptococcus aureus, Cryptococcus carnescens and Cryptococcus peneaus

Fifteen strains of the Cryptococcus laurentii complex were reclassified based on sequence analyses of 18S rDNA, the D1/D2 region of the 26S rDNA and the internal transcribed spacer regions, as well as physiological and biochemical properties. The strains were divided into phylogenetic groups I and II. The type strain of C. laurentii (CBS 139T=ATCC 18803T=JCM 9066T=MUCL 30398T=NRRL Y-2536T) was in phylogenetic group I. Phylogenetic group II, which was phylogenetically distant from phylogenetic group I, clustered with Cryptococcus dimennae and Bullera globispora. In phylogenetic group I, the type strain of Torula aurea (CBS 318T=ATCC 32063T=IFO 0372T=NRRL Y-1582T) appeared to be a separate species from C. laurentii, and the designation Cryptococcus aureus comb. nov. is proposed for Torula aurea. Cryptococcus flavescens (formerly Torula flavescens, type strain CBS 942T=ATCC 10668T=DBVPG 6007T=MUCL 30414T) was treated as a synonym of C. laurentii; however, this is a distinct species. The type strains of Torulopsis carnescens (CBS 973T=ATCC 32064T=MUCL 30641T=NRRL Y-1503T), Rhodotorula peneaus (CBS 2409T=ATCC 13546T=MUCL 30643T=NRRL Y-2005T) and Cryptococcus victoriae belonged to phylogenetic group II. Two new combinations, Cryptococcus carnescens comb. nov. (type strain CBS 973T=ATCC 32064T=MUCL 30641T=NRRL Y-1503T) and Cryptococcus peneaus comb. nov. (type strain CBS 2409T=ATCC 13546T=MUCL 30643T=NRRL Y-2005T), are proposed from this group.

Molecular systematics of the dimorphic ascomycete genus Taphrina

The ascomycete genus Taphrina Fries comprises nearly 100 species recognized by their mycelial states when parasitic on different vascular plants. Whereas the filamentous state is strictly phytoparasitic, the yeast state is saprobic and can be cultured on artificial media. Taphrina species are differentiated mainly on the basis of host range and geographical distribution, type and site of infection and morphology of the sexual stage in infected tissue. However, there has been little progress in the systematics of the genus in recent years, mainly because of the scarcity of molecular studies and available cultures. The main aim of the present study was the reappraisal of species boundaries in Taphrina based on the genetic characterization of cultures (yeast states) that represent about one-third of the currently recognized species. The molecular methods used were (i) PCR fingerprinting using single primers for microsatellite regions and (ii) determination of nucleotide sequences of two approx. 600 bp nuclear rDNA regions, the 5' end of the 26S rRNA gene (D1/D2 domains) and the internal transcribed spacer region (which includes the 5.8S rRNA gene). Sequencing results confirmed the monophyly of the genus (with the probable exclusion of Taphrina vestergrenii) and the combined analysis of the two methods corroborated, in most cases, separation of species defined on the basis of conventional criteria. However, genetic heterogeneity was found within some species and conspecificity was suggested for strains that have been deemed to represent distinct species. Sequences from the ITS region displayed a higher degree of divergence than those of the D1/D2 region between closely related species, but were relatively conserved within species (> 99% identity) and were thus more useful for the effective differentiation of Taphrina species. The results further allowed other topics to be addressed such as the correlation between the molecular phylogenetic clustering of certain species and the respective host plant family and the significance of molecular methods in the accurate diagnosis of the different diseases caused by Taphrina species.

Ribosomal DNA and resolution of branching order among the ascomycota: how many nucleotides are enough?

Molecular phylogenies for the fungi in the Ascomycota rely heavily on 18S rRNA gene sequences but this gene alone does not answer all questions about relationships. Particularly problematical are the relationships among the first ascomycetes to diverge, the Archiascomycetes, and the branching order among the basal filamentous ascomycetes, the Euascomycetes. Would more data resolve branching order? We used the jackknife and bootstrapping resampling approach that constitutes the "pattern of resolved nodes" method to address the relationship between number of variable sites in a DNA sequence alignment and support for taxonomic clusters. We graphed the effect of increasing sizes of subsamples of the 18S rRNA gene sequences on bootstrap support for nodes in the Ascomycota tree. Nodes responded differently to increasing data. Some nodes, those uniting the filamentous ascomycetes for example, would still have been well supported with only two thirds of the 18S rRNA gene. Other nodes, like the one uniting the Archiascomycetes as a monophyletic group, would require about double the number of variable sites available in the 18S gene for 95% neighbor-joining bootstrap support. Of the several groups emerging at the base of the filamentous ascomycetes, the Pezizales receive the most support as the first to diverge. Our analysis suggests that we would also need almost three times as much sequence data as that provided by the 18S gene to confirm the basal position for the Pezizales and more than seven times as much data to resolve the next group to diverge. If more data from other genes show the same pattern, the lack of resolution for the filamentous ascomycetes may indicate rapid radiation within this clade.

Killer activity of Tilletiopsis albescens Gokhale: taxonomic and phylogenetic implication

Killer activity expressed at pH values ranging from 3.5 to 8.0 was found in the Tilletiopsis albescens VKM-2822. Its killer phenotype was cureless. The toxin excreted with a molecular mass above 10 kDa is fungicidal, thermolabile, sensitive to proteinase K and was specified as a mycocin. The latter does not act against ascomycetous, sporidiobolaceous and tremellaceous yeasts. In contrast to all other Rhodotorula species, Rh. bacarum, Rh. hinnulea and Rh. phylloplana are sensitive to the mycocin studied. Also, its killing pattern includes the species of the genera Exobasidium, Farysia, Protomyces, Pseudozyma, Sporisorium, Taphrina and Ustilago. The host range of T. albescens mycocin is discussed from taxonomic and phylogenetic viewpoints.

Multiple origins of fungal group I introns located in the same position of nuclear SSU rRNA gene

The archiascomycetous fungus Protomyces pachydermus has two group I introns within the nuclear small subunit (nSSU) rRNA gene. One of these introns has an internal open reading frame (ORF) that encodes a predicted protein of 228 amino acid residues. On the other hand, Protomyces macrosporus has two group I introns that insert at the same positions as P. pachydermus, which have no ORF. Each alignment was constructed with Protomyces group I introns located in the same position and other introns retrieved by the BLAST Search. Each phylogenetic tree based on the alignment shows that Protomyces introns are monophyletic but the relationships among fungal introns do not reflect on the fungal phylogeny. Therefore, it is suggested that two different horizontal transfers of group I introns occurred at the early stage of Protomyces species diversification.