Heteroduplex mobility assay of the D1/D2 region of the 26S rDNA for differentiation of Saccharomyces species

Bullera vrieseae sp. nov., a tremellaceous yeast species isolated from bromeliads

Two independent surveys of yeasts associated with different bromeliads in different Brazilian regions led to the proposal of a novel yeast species, Bullera vrieseae sp. nov., belonging to the Tremellales clade (Agaricomycotina, Basidiomycota). Analysis of the sequences in the internal transcribed spacer (ITS) region and D1/D2 domain of the LSU rRNA gene suggested affinity to a phylogenetic lineage that includes Bullera miyagiana and Bullera sakaeratica. Six isolates of the novel species were obtained from different bromeliads and regions in Brazil. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species differs from B. miyagiana and B. sakaeratica by 85 and 64 nt substitutions, respectively and by more than 75 nt substitutions in the ITS region. Phenotypically, Bullera vrieseae sp. nov. can be distinguished from both species based on the assimilation of meso-erythritol, which was negative for B. vrieseae sp. nov. but positive for the others, assimilation of d-glucosamine, which was positive for B. vrieseae sp. nov. but negative for B. miyagiana and of l-sorbose, which was negative for B. vrieseae sp. nov. but positive for B. sakaeratica. The novel species Bullera vrieseae sp. nov. is proposed to accommodate these isolates. The type strain of Bullera vrieseae sp. nov. is UFMG-CM-Y379T (BRO443T; ex-type CBS 13870T).

(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts?

In microbiology, identification of all isolates by sequencing is still unfeasible in small research laboratories. Therefore, many yeast diversity studies follow a screening procedure consisting of clustering the yeast isolates using MSP-PCR fingerprinting, followed by identification of one or a few selected representatives of each cluster by sequencing. Although this procedure has been widely applied in the literature, it has not been properly validated. We evaluated a standardized protocol using MSP-PCR fingerprinting with the primers (GTG)₅ and M13 for the discrimination of wine associated yeasts in South Brazil. Two datasets were used: yeasts isolated from bottled wines and vineyard environments. We compared the discriminatory power of both primers in a subset of 16 strains, choosing the primer (GTG)₅ for further evaluation. Afterwards, we applied this technique to 245 strains, and compared the results with the identification obtained by partial sequencing of the LSU rRNA gene, considered as the gold standard. An array matrix was constructed for each dataset and used as input for clustering with two methods (hierarchical dendrograms and QAPGrid layout). For both yeast datasets, unrelated species were clustered in the same group. The sensitivity score of (GTG)₅ MSP-PCR fingerprinting was high, but specificity was low. As a conclusion, the yeast diversity inferred in several previous studies may have been underestimated and some isolates were probably misidentified due to the compliance to this screening procedure.

Hannaella pagnoccae sp. nov., a tremellaceous yeast species isolated from plants and soil

Several independent surveys of yeasts associated with different plant materials and soil led to the proposal of a novel yeast species belonging to the Tremellales clade (Agaricomycotina, Basidiomycota). Analysis of the sequences of the D1/D2 domains and internal transcribed spacer region of the large subunit of the rRNA gene suggested affinity to a phylogenetic lineage that includes Hannaella coprosmaensis, Hannaella oryzae and Hannaella sinensis. Thirty-two isolates were obtained from different sources, including bromeliads, nectar of Heliconia psittacorum (Heliconiaceae), flowers of Pimenta dioica (Myrtaceae), roots and leaves of sugar cane (Saccharum spp.) in Brazil, leaves of Cratoxylum maingayi, Arundinaria pusilla and Vitis vinifera in Thailand, soil samples in Taiwan, and prairie soil in the USA. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species differs from Hannaella coprosmaensis and Hannaella oryzae by 36 and 46 nt substitutions, respectively. A novel species is suggested to accommodate these isolates, for which the name Hannaella pagnoccae sp. nov. is proposed. The type strain is BI118(T) ( = CBS 11142(T) = ATCC MYA-4530(T)).

Sympodiomycopsis yantaiensis sp. nov., a basidiomycetous yeast isolated from insect frass

Two strains (NYNU 121010T and NYNU 121032) of a novel basidiomycetous yeast species belonging to the genus Sympodiomycopsis were isolated from insect frass collected from trunks of a pagoda tree (Sophora japonica L.) in Yantai, Shandong province, east China. The sequence analyses of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region indicated that the closest relatives were Sympodiomycopsis kandeliae FIRDI 007T, Sympodiomycopsis paphiopedili CBS 7429T and Sympodiomycopsis sp. S6A. The D1/D2 sequences of the novel strains differed by 12 nt substitutions (2 %) from the type strain of S. kandeliae, and by 13 nt substitutions (2.2 %) from the type strain of S. paphiopedili and from Sympodiomycopsis sp. S6A. The novel strains differed from closely related species by more than 4.6 % substitutions in the ITS region. The novel strains can also be distinguished from S. kandeliae and S. paphiopedili on the basis of a number of morphological and physiological characteristics and represent a novel species in the genus Sympodiomycopsis, for which the name Sympodiomycopsis yantaiensis sp. nov. is proposed. The type strain is NYNU 121010T ( = CICC 32998T = CBS 12813T). The Mycobank deposit number is MB 804119.

Wickerhamomyces mori sp. nov., an anamorphic yeast species found in the guts of wood-boring insect larvae

A novel anamorphic yeast species is described to accommodate three isolates recovered from the guts of three different wood-boring insect larvae collected in Henan, central China. On the basis of sequence analyses of the D1/D2 domains of the large-subunit rRNA gene and the internal transcribed spacer regions, the three strains are assigned to a novel species of the genus Wickerhamomyces, although the formation of ascospores was not observed. These strains also exhibited a number of distinct morphological and physiological characteristics that clearly differentiated them from Wickerhamomyces mucosus, Candida odintsovae and Wickerhamomyces rabaulensis, the most closely related species. In view of the phenotypic differences and unique rRNA gene sequences, we consider that these three isolates represent a novel species of the genus Wickerhamomyces, Wickerhamomyces mori sp. nov. The type strain is NYNU 1216T ( = CICC 1983T  = CBS 12678T).

Cryptococcus nanyangensis sp. nov., a new basidiomycetous yeast isolated from the gut of wood-boring larvae

Two strains of a novel basidiomycetous yeast species were isolated from the gut of wood-boring larvae collected in the Baotianman Nature Reserve, the central China. Sequence analysis of the D1/D2 domains of the large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) regions showed that these yeasts belong to the Bulleromyces clade and formed a cluster together with eleven undescribed Cryptococcus species. The novel species differed from its closest known species, Cryptococcus rajasthanensis, by 3.3 % divergence (15 substitutions and 6 gaps over 630 bases) in the D1/D2 domains, and by 13.4 % divergence (41 substitutions and 27 gaps over 508 bases) in the ITS regions. Physiologically, the fermentation of glucose, galactose, sucrose, trehalose, and raffinose in Durham tubes was observed for the strains of this new yeast. Based on the phenotypical and molecular characteristics presented, the two strains are proposed as a new species, Cryptococcus nanyangensis sp. nov., with the type strain KCY-1(T) (=CICC 1976(T) = CBS 12474(T)).

Candida sanyaensis sp. nov., an ascomycetous yeast species isolated from soil

Strains representing a novel ascomycetous yeast species, Candida sanyaensis, were isolated from soil samples collected on Hainan Island and Taiwan Island in China. Analysis of the D1/D2 domains of the large subunit (LUS) rRNA gene and internal transcribed spacer (ITS) regions of these strains showed that this species was related to Candida tropicalis and Candida sojae, their closest relatives. C. sanyaensis differed by three substitutions and one gap from C. tropicalis, and by four substitutions and one gap from C. sojae, in the D1/D2 domain sequences. However, the ITS sequences of C. sanyaensis were quite divergent from the latter two species, showing that it is a genetically separate species. The novel strains were also found to have very similar PCR-fingerprinting profiles which were quite distinct from those of C. tropicalis and C. sojae strains. The type strain of C. sanyaensis is HN-26(T) (= CICC 1979(T) = CBS 12637(T)).

Candida ficus sp. nov., a novel yeast species from the gut of Apriona germari larvae

A novel yeast species is described based on three strains from the gut of wood-boring larvae collected in a tree trunk of Ficus carica cultivated in parks near Nanyang, central China. Phylogenetic analysis based on sequences of the D1/D2 domains of the large subunit rRNA gene showed that these strains occurred in a separate clade that was genetically distinct from all known ascomycetous yeasts. In terms of pairwise sequence divergence, the novel strains differed by 15.3% divergence from the type strain of Pichia terricola, and by 15.8% divergence from the type strains of Pichia exigua and Candida rugopelliculosa in the D1/D2 domains. All three are ascomycetous yeasts in the Pichia clade. Unlike P. terricola, P. exigua and C. rugopelliculosa, the novel isolates did not ferment glucose. The name Candida ficus sp. nov. is proposed to accommodate these highly divergent organisms, with STN-8(T) (=CICC 1980(T)=CBS 12638(T)) as the type strain.

Dipodascus capitatus (Geotrichum capitatum): infecção sistêmica fatal em paciente com leucemia mielocítica aguda

As infecções causadas por Dipodascus capitatus são raras e de difícil tratamento. Aqui se relata um caso em paciente com leucemia mielocítica aguda. O isolamento fúngico ocorreu a partir de hemocultura e a identificação fenotípica baseou-se em métodos micológicos clássicos; a identificação genotípica foi realizada através do sequenciamento da região D1/D2 do 26 rDNA. Os testes de suscetibilidade foram realizados através do Etest® e microdiluição em caldo. A antifungicoterapia foi ineficaz, registrando-se óbito da paciente no 17° dia após o diagnóstico. Os autores comparam o caso com relatos similares e discutem a emergência destas infecções bem como suas dificuldades diagnósticas e terapêuticas.

Barcode-like heteroduplex DNA pattern as an aid for rapid identification of anthracnose fungi

We have shown the usefulness of the heteroduplex mobility assay (HMA) for phylogenetic analysis and for the discrimination of closely related Colletotrichum species. Because the heteroduplex mobility of a tested strain shows a unique banding pattern that is the function of the sequence of the referred strain, we further explored the potential use of heteroduplex DNA patterns (HPs) as DNA fingerprints for the identification of these fungi. The 29 Colletotrichum strains previously identified by HMA to be taxonomic members of CG, CA, CM, CC and CL species groups were re-examined with an emphasis on their unique heteroduplex banding patterns. The species attributes of these tested strains were characterized by HMA using ITS fragments amplified from six representative Colletotrichum strains as pairwise compared references. By comparing the unique homoduplex and heteroduplex banding patterns of each tested strain on a polyacrylamide gel with those of the respective reference strain, the species identity of tested strains was determined. The obtained barcode-like HPs classified these 29 Colletotrichum strains into 6 distinctive groups: CG1, CG2, CA, CM, CC and CL. Notably, the HPs differentiated strains CG1 and CG2, which differed in their ITS sequences by only six bases. The presented results revealed that the species-characteristic barcode-like HP classification of ITS regions is a relatively rapid and valuable system for species identification of Colletotrichum species. The potential use of the established barcode-like system for the identification of anthracnose fungi and other fungal pathogens is discussed.

Candida aechmeae sp. nov. and Candida vrieseae sp. nov., novel yeast species isolated from the phylloplane of bromeliads in Southern Brazil

Two novel yeast species, Candida aechmeae sp. nov. and Candida vrieseae sp. nov., were isolated from bromeliads in Itapuã Park, Rio Grande do Sul, Brazil. These species are genetically isolated from all other currently recognized ascomycetous yeasts based on their sequence divergence in the D1/D2 domain of the LSU rRNA gene. C. aechmeae sp. nov. is phylogenetically close to Candida ubatubensis, a species also isolated from bromeliads in Brazil, but the novel species can be differentiated on the basis of differences in the D1/D2 domain and positive results for the assimilation of l-arabinose, raffinose, inulin and citrate. Candida vrieseae sp. nov. is phylogenetically placed in a clade near Candida membranifaciens that is composed of several species associated with insects, but the novel species can be differentiated from them by the D1/D2 and ITS gene sequences, positive results for the assimilation of nitrite and a negative result for the assimilation of ethylamine. The type strain for Candida aechmeae sp. nov. is BI153(T) (=CBS 10831(T)=NRRL Y-48456(T)) and the type strain for C. vrieseae sp. nov. is BI146(T) (=CBS 10829(T)=NRRL Y-48461(T)).

Cryptococcus terrestris sp. nov., a tremellaceous, anamorphic yeast phylogenetically related to Cryptococcus flavescens

Cryptococcus terrestris sp. nov. (Basidiomycota, Agaricomycotina, Tremellomycetes, Tremellales) is typified by CJDX4 Y23(T) (=CBS 10810(T) =NRRL Y-48451(T)), isolated from forest soil in Oklahoma, USA. This species is most readily identified by the sequence of the D1/D2 domain region of the 26S rDNA and ITS (internal transcribed spacer) region. Additional strains from Oklahoma (C107DX4 Y11 =CBS 10813 =NRRL Y-48452) and Brazil (Ep11c =CBS 10812 =NRRL Y-48454; 56e =CBS 10811 =NRRL Y-48453) either had identical sequences or differed minimally. C. terrestris differs physiologically from the most closely related species, Cryptococcus flavescens, by the weak or delayed assimilation of ribose and salicin, and differs from Cryptococcus aureus by the utilization of nitrate and nitrite and growth in vitamin-free medium.

Trichosporon insectorum sp. nov., a new anamorphic basidiomycetous killer yeast

Three killer yeasts, isolated from the gut of insects in Panama and artisanal cheese in Brazil, were shown to be related to the Ovoides clade of the genus Trichosporon. Sequencing of the D1/D2 region of the LSU rDNA and physiological characterization revealed a distinct taxonomic position in relation to known species of the genus. Conspecificity of the three killer isolates was reinforced by similar M13 fingerprinting and killer profiles. We propose a new species in this genus: Trichosporon insectorum. The type strain is CBS 10422(T) (syn. NRRL Y-48120). This anamorphic species produces arthroconidia but not appressoria, and its killer character seems to be associated with dsRNA.

Inhibition of clinical and environmental Cryptococcus neoformans isolates by two Brazilian killer yeasts

Two killer yeast strains (HB55 and HB88) capable of inhibiting human pathogenic fungi were isolated from leaves of Hibiscus rosa-sinensis in Brazil. These isolates were identified by conventional methods and sequencing of the D1/D2 region of the 26S rDNA as Kodamaea ohmeri. They inhibited all Cryptococcus neoformans (vars. neoformans, grubii and gattii) strains tested, including reference, clinical and environmental isolates. The killer phenotype was not cured by thermal treatment.

Heteroduplex mobility assay of the 26S rDNA D1/D2 region for differentiation of clinically relevant Candida species

The Heteroduplex Mobility Assay (HMA) method using the PCR amplified D1/D2 region of the 26S rDNA was tested for the differentiation of clinically relevant Candida species. Strains belonging to the same species are not expected to form heteroduplexes in this assay when their PCR products are mixed. D1/D2 HMA experiments between all Candida type strains tested showed heteroduplex formation, including Candida albicans and Candida dubliniensis. There was no heteroduplex formation when most clinical and non-type strains were tested against the type strain of their presumptive species, except when C. albicans WVE and C. dubliniensis TAI were analysed. Additional HMA experiments, phenotypic characterisation, and D1/D2 sequencing identified these isolates as Candida tropicalis and Candida parapsilosis, respectively. HMA provides a rapid and relatively simple molecular tool for the differentiation of potentially pathogenic Candida species.

Heteroduplex mobility assay for the identification of Listeria sp and Listeria monocytogenes strains: application to characterisation of strains from sludge and food samples

One hundred and ten Listeria sp. isolates from sewage sludge were identified according to phenotypic and genotypic methods. The Listeria sp. strains isolated from five types of sludge from three sewage treatment plants in Angers (France) and the surrounding area included L. monocytogenes (55.5%), L. innocua (29.1%), L. seeligeri (13.6%) and L. welshimeri (1.8%). The majority of L. monocytogenes strains belonged to serotypes 4b, 1/2b and 1/2a. Moreover, a heteroduplex mobility assay based on the 16S rRNA sequences was tested for its ability to identify the six species of the genus Listeria. This study, performed on 283 Listeria sp. strains from human, food and sewage sludge samples, showed that all the species were distinguishable from one another. L. innocua and L. seeligeri showed respectively three and two distinct banding patterns. Within L. monocytogenes, four groups (I-IV) were defined. The majority of food and environmental isolates were clustered in group I and it is noteworthy that group IV clustered epidemiologic isolates and strains belonging to serotypes 4b, 1/2a and 1/2b.