Spencermartinsiella henanensis fa., sp. nov., a novel yeast species isolated from rotting wood.

Two yeast strains (NYNU 211162 and NYNU 211275) were isolated from rotting wood collected in the Baotianman Nature Reserve, Henan Province, central China. Phylogenetic analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region revealed that the strains represent a phylogenetically distinct species within the genus Spencermartinsiella. The name Spencermartinsiella henanensis fa., sp. nov. is proposed for this species with holotype CICC 33543T (Mycobank MB 851142). S. henanensis sp. nov. differed by only 3 nt (~0.5 %) substitutions from the closest known species S. europaea NCAIM Y.01817T in the D1/D2 domain, but by 33 nt (~6 %) substitutions, 34 nt (~3.8 %) substitutions, 30 nt (~5.6 %) substitutions and 75 nt (~9.9 %) substitutions in the ITS region and the partial TEF1, COXII and RPB2 genes. Additionally, S. henanensis sp. nov. can be physiologically distinguished from S. europaea by its ability to assimilate inulin, inability to assimilate ethylamine and cadaverine, and incapability of growth at 30 °C.

Spencermartinsiella nicolii sp. nov., a potential opportunistic pathogenic yeast species isolated from rotting wood in Brazil.

Nineteen isolates representing a candidate for a novel yeast species belonging to the genus Spencermartinsiella were recovered from rotting wood samples collected at different sites in Atlantic Rainforest and Amazonian Forest ecosystems in Brazil. Similarity search of the nucleotide sequence of the intergenic spacer (ITS)-5.8S and large subunit D1/D2 regions of the ribosomal gene cluster showed that this novel yeast is closely related to Spencermartinsiella cellulosicola. The isolates differ by four nucleotide substitutions in the D1/D2 domain and six substitutions and 31 indels in the ITS region from the holotype of S. cellulosicola. Phylogenomic analysis based on 1474 single-copy orthologues for a set of Spencermartinsiella species whose whole genome sequences are available confirmed that the novel species is phylogenetically close to S. cellulosicola. The low average nucleotide identity value of 83% observed between S. cellulosicola and the candidate species confirms that they are distinct. The novel species produced asci with hemispherical ascospores. The name Spencermartinsiella nicolii sp. nov. is proposed. The holotype is CBS 14238T. The MycoBank number is MB855027. Interestingly, the D1/D2 sequence of the S. nicolii was identical to that of an uncultured strain of Spencermartinsiella causing systemic infection in a male adult crocodile (Crocodylus niloticus). The characterization of some virulence factors and antifungal susceptibility of S. nicolii isolates suggest that this yeast may be an opportunistic pathogen for animals, including humans; the isolates grow at 37 °C.

Wickerhamiella lachancei f.a. sp. nov., a novel ascomycetous yeast species isolated from flowers of Lantana camara in India.

Two isolates representing a novel species of the genus Wickerhamiella were obtained in India from nectar of flowers of Lantana camara, an ornamental exotic species native to Central and South America. Phylogenetic analyses of the D1/D2 domain of the 26S large subunit (LSU) rRNA gene, internal transcribed spacer (ITS) region, and physiological characteristics, supported the recognition of the novel species, that we designate Wickerhamiella lachancei sp. nov (MycoBank no. MB851709), with MCC 9929T as the holotype and PYCC 10003T as the isotype. Considering pairwise sequence similarity, the type strain of the novel species differs from the type strain of the most closely related species, Wickerhamiella drosophilae CBS 8459T, by 16 nucleotide substitutions and two gaps (3.9 % sequence variation) in the D1/D2 region (560 bp compared) and 28 nucleotide substitutions and five gaps (7.22 % sequence variation) in the ITS region (444 bp compared).

The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species.

This study investigated the diversity of yeast species associated with rotting wood in Brazilian Amazonian rainforests. A total of 569 yeast strains were isolated from rotting wood samples collected in three Amazonian areas (Universidade Federal do Amazonas-Universidade Federal do Amazonas [UFAM], Piquiá, and Carú) in the municipality of Itacoatiara, Amazon state. The samples were cultured in yeast nitrogen base (YNB)-d-xylose, YNB-xylan, and sugarcane bagasse and corncob hemicellulosic hydrolysates (undiluted and diluted 1:2 and 1:5). Sugiyamaella was the most prevalent genus identified in this work, followed by Kazachstania. The most frequently isolated yeast species were Schwanniomyces polymorphus, Scheffersomyces amazonensis, and Wickerhamomyces sp., respectively. The alpha diversity analyses showed that the dryland forest of UFAM was the most diverse area, while the floodplain forest of Carú was the least. Additionally, the difference in diversity between UFAM and Carú was the highest among the comparisons. Thirty candidates for new yeast species were obtained, representing 36% of the species identified and totaling 101 isolates. Among them were species belonging to the clades Spathaspora, Scheffersomyces, and Sugiyamaella, which are recognized as genera with natural xylose-fermenting yeasts that are often studied for biotechnological and ecological purposes. The results of this work showed that rotting wood collected from the Amazonian rainforest is a tremendous source of diverse yeasts, including candidates for new species.

Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products.

In this review, we describe the genomic and physiological features of the yeast species predominantly isolated from Nuruk, a starter for traditional Korean rice wines, and Jang, a traditional Korean fermented soy product. Nuruk and Jang have several prevalent yeast species, including Saccharomycopsis fibuligera, Hyphopichia burtonii, and Debaryomyces hansenii complex, which belong to the CUG clade showing high osmotic tolerance. Comparative genomics revealed that the interspecies hybridization within yeast species for generating heterozygous diploid genomes occurs frequently as an evolutional strategy in the fermentation environment of Nuruk and Jang. Through gene inventory analysis based on the high-quality reference genome of S. fibuligera, new genes involved in cellulose degradation and volatile aroma biosynthesis and applicable to the production of novel valuable enzymes and chemicals can be discovered. The integrated genomic and transcriptomic analysis of Hyphopichia yeasts, which exhibit strong halotolerance, provides insights into the novel mechanisms of salt and osmo-stress tolerance for survival in fermentation environments with a low-water activity and high-concentration salts. In addition, Jang yeast isolates, such as D. hansenii, show probiotic potential for the industrial application of yeast species beyond fermentation starters to diverse human health sectors.

Hanseniaspora menglaensis f.a., sp. nov., a novel apiculate yeast species isolated from rotting wood.

Two apiculate strains (NYNU 181072 and NYNU 181083) of a bipolar budding yeast species were isolated from rotting wood samples collected in Xishuangbanna Tropical Rainforest in Yunnan Province, southwest PR China. On the basis of phenotypic characteristics and the results of phylogenetic analysis of the D1/D2 domain of the large subunit (LSU) rRNA, internal transcribed spacer (ITS) region and the actin (ACT1) gene, the two strains were found to represent a single novel species of the genus Hanseniaspora, for which the name Hanseniaspora menglaensis f.a., sp. nov. (holotype CICC 33364T; MycoBank MB 847437) is proposed. In the phylogenetic tree, H. menglaensis sp. nov. showed a close relationship with Hanseniaspora lindneri, Hanseniaspora mollemarum, Hanseniaspora smithiae and Hanseniaspora valbyensis. H. menglaensis sp. nov. differed from H. lindneri, the most closely related known species, by 1.2 % substitutions in the D1/D2 domain, 2.5 % substitutions in the ITS region and 5.4 % substitutions in the ACT1 gene, respectively. Physiologically, H. menglaensis sp. nov. can also be distinguished from H. lindneri by its ability to assimilate d-gluconate.

Danielozyma pruni sp. nov., an asexual yeast species isolated from insect frass.

Two strains (NYNU 218101 and NYNU 218104) of an asexual yeast species were isolated from insect frass collected in insect tunnels of red leaf plum trees in the Henan Province, central China. Molecular phylogenetic analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer (ITS) region showed that these two strains belonged to the genus Danielozyma, with Danielozyma litseae as the closest known species. They differed from the type strain of D. litseae by 0.6 % substitutions (three substitutions and one gap) in the D1/D2 domain and by 5.1 % substitutions (19 substitutions and six gaps) in the ITS region, respectively. When compared with the partial ACT1, TEF1 and RPB1 gene sequences, they differed by 3 % (26 substitutions), 2.7 % (25 substitutions) and 9 %(54 substitutions) from D. litseae NRRL YB-3246T in these regions. Physiologically, they also differed from its closest known species D. litseae based on the ability to assimilate inulin and galactitol, as well as to grow in 0.1 % cycloheximide and its inability to ferment maltose and raffinose. In order to classify the two new isolates based on morphological and molecular evidence, we proposed the description of a novel species Danielozyma pruni sp. nov. with strain JCM 35735T as holotype (Mycobank MB 849101).

Hannaella floricola sp. nov., a novel basidiomycetous yeast species isolated from a flower of Lantana camara in Portugal.

During a survey of floricolous yeasts in Portugal, a basidiomycetous yeast representing a novel species in the genus Hannaella was isolated in Portugal from the flower of Lantana camara, an ornamental exotic species native to Central and South America. A combination of phylogenetic analyses of DNA barcode sequences used in yeast molecular systematics, namely the D1/D2 domain and the complete internal transcribed spacer (ITS) region supported the recognition of a new species of Hannaella, that we designate Hannaella floricola sp. nov. (ex-type strain PYCC 9191T=CBS 18097T). Although the assignment of the new species to the genus Hannaella was evident, the detection of its closest relatives appeared more problematic. Nevertheless, our analyses suggested that H. floricola sp. nov. belongs a clade that also includes H. coprosmae, H. oryzae and H. surugaensis, together four candidate novel species. In addition we provide the molecular identification of several unidentified strains whose D1/D2 and ITS sequences are available from GenBank.

Metschnikowia ahupensis f.a., sp. nov., a new yeast species isolated from the gut of the wood-feeding termite Nasutitermes sp.

The gut of xylophagous insects such as termites harbours various symbiotic micro-organisms, including many yeast species. In a taxonomic study of gut-associated yeasts, two strains (ATS2.16 and ATS2.18) were isolated from the gut of the wood-feeding termite Nasutitermes sp. in Maharashtra, India. Morphological and physiological characteristics and sequence analyses of the ITS and D1/D2 region of the large subunit rRNA gene revealed that these two strains represent a novel asexual ascomycetous yeast species in the genus Metschnikowia. The species differs from some of its close affiliates in the genus in its inability to utilize ethanol and succinate as the sole carbon source and growth in high sugar concentrations (up to 50 % glucose). In contrast to most members of Metschnikowia, the formation of ascospores was not observed on various sporulation media. Moreover, whole-genome sequencing was used to further confirm the novelty of this species. When compared with other large-spored Metschnikowia species, average nucleotide identity values of 79-80 % and digital DNA-DNA hybridization values of 16-17 % were obtained. The name Metschnikowia ahupensis f.a., sp. nov. is proposed to accommodate this novel yeast species, with ATS2.16 as the holotype and strains NFCCI 4949, MTCC 13085 and PYCC 9152 as isotypes. The MycoBank number is MB 844210.

Diddensiella parasantjacobensis f.a., sp. nov., a yeast species from forest habitats.

Six conspecific yeast strains, representing an undescribed species, were isolated from rotten wood collected in different locations in Hungary and Germany and an additional one from fungal fruiting body in Taiwan. The seven strains share identical nucleotide sequences in the D1/D2 domain of the nuclear large subunit (LSU) rRNA gene. The Hungarian and Taiwanese isolates share identical internal transcribed spacer (ITS) sequences as well, while the two German isolates differ from them merely by three substitutions and four indels in this region. The investigated strains are very closely related to Diddensiella santjacobensis. Along their LSU D1/D2 domain they differ only by one substitution from the type strain of D. santjacobensis. However, in the ITS region of Hungarian and Taiwanese strains we detected 3.5 % divergence (nine substitutions and nine indels) between the undescribed species and D. santjacobensis, while the German strains differed by 13 substitutions and nine indels from D. santjacobensis. This ITS sequence divergence has raised the possibility that the strains investigated in this study may represent a different species from D. santjacobensis. This hypothesis was supported by comparisons of partial translation elongation factor 1-α (EF-1α) and cytochrome oxidase II (COX II) gene sequences. While no difference and 1-2 substitutions among the partial EF-1α and COX II gene sequences of the strains of the undescribed species, respectively, were detected; the undescribed species differ by about 4 % (36 substitutions) and 10 % (50-51 substitutions) from D. santjacobensis in these regions. Parsimony network analysis of the partial COX II gene sequences also separated the investigated strains from the type strain of D. santjacobensis. In this paper we propose Diddensiella parasantjacobensis f.a., sp. nov. (holotype: NCAIM Y.02121; isotypes: CBS 17819, DSM 114156) to accommodate the above-noted strains.

Carbon and nitrogen sources consumption by ale and lager yeast strains: a comparative study during fermentation.

The rapid and efficient consumption of carbon and nitrogen sources by brewer's yeast is critical for the fermentation process in the brewing industry. The comparison of the growth characterizations of typical ale and lager yeast, as well as their consumption preference to carbon and nitrogen sources were investigated in this study. Results showed that the ale strain grew faster and had a more extended stationary phase than the lager strain. However, the lager strain was more tolerant to the stressful environment in the later stage of fermentation. Meanwhile, the ale and lager yeast strains possessed varying preferences for metabolizing the specific fermentable sugar or free amino acid involved in the wort medium. The lager strain had a strong capacity to synthesize the extracellular invertase required for hydrolyzing sucrose as well as a strong capability to metabolize glucose and fructose. Furthermore, the lager strain had an advantage in consuming Lys, Arg, Val, and Phe, whereas the ale strain had a higher assimilation rate in consuming Tyr. These findings provide valuable insights into selecting the appropriate brewer's yeast strain based on the wort components for the industrial fermentation process. KEY POINTS: • The lager strain is more tolerant to the stressful environment. • The lager strain has the great capability to synthesize the extracellular invertase. • The assimilation efficiency of free amino acid varies between ale and lager.

Phylogenies in yeast species descriptions: In defense of neighbor-joining.

The neighbor-joining (NJ) method of tree inference is examined, with special attention to its use in yeast species descriptions. How the often-vilified method works is often misunderstood. More importantly, given the right kind of data, its output is a phylogram that illustrates a hypothetical phylogeny that is just as credible as that obtained by any other method. And as with any other method, the result is greatly affected by sampling intensity, particularly the number of aligned positions used for analysis. I address various allegations, including the claim that the method is phenetic, and, therefore, not phylogenetic. I argue that NJ is the most suitable tree inference method to use in yeast species descriptions, primarily because it is best at visually preserving the extent of sequence divergence between close relatives, which continues to be the primary criterion for yeast species delineation. The relevance of bootstraps in the application of the phylogenetic species concept is discussed.

Nakazawaea odontotermitis f.a., sp. nov., a novel yeast isolated from the gut of Odontotermes horni in India.

Three strains, SMT1.3, SMT1.10, and SMT2.2, representing a novel asexual ascomycetous yeast species, were isolated from the gut of a termite Odontotermes horni in Maharashtra, India. Phylogenetic analyses of the LSU, ITS, and SSU sequences revealed that they belonged to the genus Nakazawaea, with N. siamensis as the closest relative. The new species differed from the type strain of N. siamensis (DMKU-RK467T) by 11 substitutions in the D1/D2 region of the large subunit (LSU) rRNA gene and by 8 substitutions and one gap in the small subunit (SSU) rRNA gene. Notable biochemical and physiological differences were also observed between N. siamensis and the new species. Hence, the species Nakazawaea odontotermitis f.a., sp. nov. is proposed. The type strain is SMT1.3 T (MTCC 13,105 = NFCCI 5011 = PYCC 9153). GenBank accession numbers of the LSU, ITS and SSU sequences of Nakazawaea odontotermitis f.a., sp. nov. are MZ234240, MZ234239, and OK384663. The MycoBank number is MB 841926.

Torulaspora jiuxiensis sp. nov., a novel yeast species isolated from rotting wood.

Two strains of a novel ascomycetous yeast species were isolated from rotting wood samples collected in Jiuxi Mountain Forest Park in Yunnan Province, southwest China. Both strains formed one or two spherical ascospores in persistent asci. Phylogenetic analysis of the concatenated sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) and the D1/D2 domain of the large subunit rRNA gene revealed that the novel strains represented a phylogenetically distinct species belonging to the genus Torulaspora. This novel species differed from the type strains of the closest known species, Torulaspora nypae and Torulaspora maleeae, by 0.9 and 1.2 % nucleotide substitutions in the D1/D2 domain and 5.3 and 6 % nucleotide substitutions in the ITS region, respectively. The novel species can also be distinguished from T. nypae and T. maleeae in terms of the ability to assimilate ribitol, succinate and citrate, and its ability to grow at 37 °C. The species name of Torulaspora jiuxiensis sp. nov. is proposed with holotype CBS 16004T (Mycobank MB 844535).

Moniliella aeria sp. nov., a novel yeast isolated from the air of a Wuliangye baijiu-making workshop.

During an investigation of the diversity of airborne yeasts in a famous Chinese baijiu fermentation workshop, two yeast strains were isolated from the air of the Wuliangye 501# baijiu-making workshop in Yibin, Sichuan Province, PR China and subjected to taxonomic analysis. The results of phylogenetic analysis of two regions of the rRNA gene cluster, the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, indicated that these strains represented a novel species of the genus Moniliella distinct from closely related species. The similarity between the novel species and the most closely related known species, Moniliella dehoogii, was 94.1 % for the D1/D2 LSU rRNA gene (30 substitutions and 12 indels out of 556 bp) and 95.6 % for the ITS region (9 substitutions and 6 indels out of 475 bp). In contrast with M. dehoogii, this novel species was able to assimilate d-ribose, l-arabinose, d-arabinose, cellobiose, d-glucono-1,5-lactone, dl-lactate, citrate, 1,2-propanediol, 2,3-butanediol and ethanol but was unable to ferment raffinose or assimilate inulin. On the basis of the results of phylogenetic analysis and the physiological characteristics, these investigated strains represent a novel species of the genus Moniliella, for which the name Moniliella aeria sp. nov. is proposed. Its holotype is CGMCC 20235T, and the MycoBank number is MB840188.

Magnusiomyces siamensis sp. nov., a yeast-like fungus isolated from food waste.

Three yeast strains, DMKU-GTSP8-6, DMKU-GTSP8-14T and DMKU-JED8-73, were isolated from food waste in Thailand. Based on the phenotypic characteristics and sequence analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, it was revealed that the three strains clustered with the Magnusiomyces/Saprochaete clade. These strains were distinguished from the closely related species Saprochaete quercus CBS 750.85, Magnusiomyces ovetensis CBS 192.55T, Magnusiomyces starmeri CBS 780.96T, Saprochaete chiloensis CBS 8187T and Magnusiomyces ingens CBS 517.90T by 11.4, 13.1, 11.9, 11.2 and 12.6 % sequence divergence in the D1/D2 domain and by 34.6, 34.5, 33.6, 33.2 and 34.9 % sequence divergence in the ITS region, respectively. The new species, which does not produce ascospores, is described as Magnusiomyces siamensis. The holotype of Magnusiomyces siamensis is TBRC 15056T, and the isotypes are DMKU-GTSP8-14T and PYCC 9023T.

Hyphopichia xiaguanensis f.a., sp. nov., an ascomycetous yeast species isolated from plant leaves.

Two strains representing a novel yeast species were isolated from plant leaves collected in the Baotianman Nature Reserve in Henan Province, central China. Phylogenetic analysis based on the concatenated sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) and the D1/D2 domain of the large subunit rRNA gene revealed that the novel species belonged to the genus Hyphopichia, although the formation of ascospores was not observed. The novel species was related most closely to Hyphopichia paragotoi CBS 13913T but they differed by 0.9 % sequence divergence (five substitutions) in the D1/D2 domain and by 3.7 % sequence divergence (seven substitutions and eight gaps) in the ITS region. Furthermore, the novel species can also be differentiated from the closely related species in some biochemical and physiological characteristics. The species name of Hyphopichia xiaguanensis f.a., sp. nov. (Holotype CBS 16668, Mycobank MB 842425) is proposed to accommodate strains NYNU 20899T and NYNU 20914.

Pichia bovicola sp. nov., a yeast species associated with small-intestinal content of cattle.

Three yeast strains, DMKU-MP6-4T, DMKU-MP2-6 and DMKU-MP5-1, were isolated from the small-intestinal content or Pia of cattle in Thailand during the investigation of yeast diversity in this habitat. According to the D1/D2 domain of the large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) region sequence analysis, these strains represent a novel yeast species in the genus Pichia. The species produced one to four ascospores per ascus with spherical to ellipsoidal shape and heterogenous in terms of size. These three strains were identical and differed from their closely related species, Pichia exigua NRRL Y-10920T by 2% (six nucleotide substitutions and five gaps) in the D1/D2 domain of the large subunit rRNA gene, while ITS region sequences differed by 3.1% (16 nucleotide substitutions and 27 gaps), 3.7% (19 nucleotide substitutions and 28 gaps) and 3.1% (16 nucleotide substitutions and 27 gaps) for DMKU-MP6-4T, DMKU-MP2-6 and DMKU-MP5-1, respectively. The name, Pichia bovicola, is proposed to accommodate these species. The holotype is DMKU-MP6-4T (TBRC 15616T=PYCC 8905T).

Tremella ananatis sp. nov. and Tremella lamprococci sp. nov., two yeast species associated with bromeliads.

Eight yeast isolates with an affinity to the genus Tremella were obtained from bromeliads from different locations in Brazil. Although the formation of basidia and basidiocarp were not observed, on the basis of the results of sequence analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) region, we suggest that these isolates represent two novel species of the genus Tremella. These yeasts are phylogenetically related to Tremella saccharicola and Tremella globispora. Therefore, we propose Tremella ananatis sp. nov. and Tremella lamprococci sp. nov. as novel yeast species of the order Tremellales (Agaricomycotina, Basidiomycota). Sequence analysis revealed that Tremella ananatis sp. nov. differs by 11 and 28 nucleotide substitutions from Tremella saccharicola in the D1/D2 sequence and ITS region, respectively. Moreover, Tremella lamprococci sp. nov. differs by 15 and 29 nucleotide substitutions from Tremella globispora in the D1/D2 sequence and ITS region, respectively. The holotypes of Tremella ananatis sp. nov. and Tremella lamprococci sp. nov. are CBS 14568T and CBS 14567T, and the MycoBank numbers are MB840480 and MB840481, respectively.

Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species.

Metabolic network reconstructions have become an important tool for probing cellular metabolism in the field of systems biology. They are used as tools for quantitative prediction but also as scaffolds for further knowledge contextualization. The yeast Saccharomyces cerevisiae was one of the first organisms for which a genome-scale metabolic model (GEM) was reconstructed, in 2003, and since then 45 metabolic models have been developed for a wide variety of relevant yeasts species. A systematic evaluation of these models revealed that-despite this long modeling history-the sequential process of tracing model files, setting them up for basic simulation purposes and comparing them across species and even different versions, is still not a generalizable task. These findings call the yeast modeling community to comply to standard practices on model development and sharing in order to make GEMs accessible and useful for a wider public.