Yeast population of the Kindo Peninsula lichens

Yeast abundance and species diversity in the lichens collected at the Kindo Peninsula (Karelia) were studied. A total of 14 lichen species analyzed belonged to the genera Bryoria, Cladonia, Hypogymnia, Icmadophila, Nephroma, Peltigera, and Ramalina. Abundance of cultured yeasts in lichens was intermediate between soil and phyllosphere. The average yeast number on lichens was ~2.5 × 10³ CFU/g, while it exceeded 8 × 10³ CFU/g on plants and reached only 1 × 10³ CFU/g in soil. Yeast population of different parts of Cladonia lichens was found to vary significantly in abundance, species diversity, and community structure. The highest yeast abundance and diversity were revealed in the growth zone. Fifteen yeast species were isolated from lichens, including 6 basidiomycetous and 9 ascomycetous ones. Unlike soils and plants, yeast population of lichens consisted mainly of ascomycetous species, with predominance of Candida sphagnicola and anamorphous yeasts of the genus Dothiora. These results show that yeasts from different taxonomic and ecological groups are a necessary component of lichens; conditions favoring the preservation and development of specific yeast communities differing from the typical soil and phyllosphere yeast complexes are formed in the lichens of northern taiga forests.     

Endophytic yeasts in <Emphasis Type="Italic">Malus domestica</Emphasis> and <Emphasis Type="Italic">Pyrus communis</Emphasis> fruits under anthropogenic impact

Yeast abundance and species diversity on the surface and in inner tissues of Malus domestica and Pyrus communis fruits under high anthropogenic impact in the city of Moscow (Russia) were studied. Results demonstrated that abundance of epiphytic yeasts on the fruits increased gradually, reaching the maximum of 3.2 × 10⁴ CFU/g on mature fruits. During summer, abundance of endophytes did not change significantly (variation near 2.5 × 10³ CFU/g) until complete maturation, while in September their numbers increased to 10⁴ CFU/g. Basidiomycetous yeasts (Filobasidium wieringae, F. magnum, Rhodotorula glutinis, and Rhodosporidiobolus colostri) predominated on the fruit surface. Ascomycetous species were the most diverse group inside the fruits, which quantitatively increased through maturation. It was found that the share of opportunistic species Candida parapsilosis in internal tissues was significant during the entire period of fruit formation and development under anthropogenic impact in the city. Specific properties of epiphytic and endophytic yeast communities developing in natural ecological niches under synanthropic conditions and anthropogenic impact are discussed.     

Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils

The effect of altitude and season on abundance and diversity of the culturable heterotrophic bacterial and yeast community was examined at four forest sites in the Italian Alps along an altitude gradient (545–2000 m). Independently of altitude, bacteria isolated at 0 °C (psychrophiles) were less numerous than those recovered at 20 °C. In autumn, psychrophilic bacterial population increased with altitude. The 1194 bacterial strains were primarily affiliated with the classes Alpha-, Beta-, Gammaproteobacteria, Spingobacteriia and Flavobacteriia. Fifty-seven of 112 operational taxonomic units represented potential novel species. Strains isolated at 20 °C had a higher diversity and showed similarities in taxa composition and abundance, regardless of altitude or season, while strains isolated at 0 °C showed differences in community composition at lower and higher altitudes. In contrast to bacteria, yeast diversity was season-dependent: site- and altitude-specific effects on yeast diversity were only detected in spring. Isolation temperature affected the relative proportions of yeast genera. Isolations recovered 719 strains, belonging to the classes Dothideomycetes, Saccharomycetes, Tremellomycetes and Mycrobotryomycetes. The presence of few dominant bacterial OTUs and yeast species indicated a resilient microbial population that is not affected by season or altitude. Soil nutrient contents influenced significantly abundance and diversity of culturable bacteria, but not of culturable yeasts.     

The yeast <Emphasis Type="Italic">Candida railenensis</Emphasis> in the fruits of English oak (<Emphasis Type="Italic">Quercus robur</Emphasis> L.)

The cotyledons of whole intact acorns were shown to contain yeasts; their number increased sharply before acorn germination. The yeasts in the cotyledons are mainly represented by one species, Candida railenensis, with the number in the germinating cotyledons reaching 10⁷ CFU/g. After germination or exocarp destruction, the cotyledons were colonized by the usual epiphytic and litter yeasts Cryptococcus albidus, Rhodotorula glutinis, and Cystofilobasidium capitatum.     

Yeast species diversity in apple juice for cider production evidenced by culture-based method

Identification of yeasts isolated from apple juices of two cider houses (one located in a plain area and one in an alpine area) was carried out by culture-based method. Wallerstein Laboratory Nutrient Agar was used as medium for isolation and preliminary yeasts identification. A total of 20 species of yeasts belonging to ten different genera were identified using both BLAST algorithm for pairwise sequence comparison and phylogenetic approaches. A wide variety of non-Saccharomyces species was found. Interestingly, Candida railenensis, Candida cylindracea, Hanseniaspora meyeri, Hanseniaspora pseudoguilliermondii, and Metschnikowia sinensis were recovered for the first time in the yeast community of an apple environment. Phylogenetic analysis revealed a better resolution in identifying Metschnikowia and Moesziomyces isolates than comparative analysis using the GenBank or YeastIP gene databases. This study provides important data on yeast microbiota of apple juice and evidenced differences between two geographical cider production areas in terms of species composition.     

Yeast Communities of the Moscow City Soils

Yeast abundance and diversity were studied in the soils (topsoil) of Moscow city: urban soils under lawn vegetation and close to the areas of household waste disposal, as well as in zonal soddy-podzolic soils (retisols) in parks (Losiny Ostrov and Izmailovo). The numbers of soil yeasts were similar in all studied urban biocenoses (on average ~3.5 × 10³ CFU/g). From all studied soils, 54 yeast species were isolated. The highest yeast diversity was found in the soils adjacent to the areas of household waste storage. Soils from different urban sites were found to have different ratios of ascomycetous and basidiomycetous yeasts: basidiomycetes predominated in urban soils under lawn vegetation, while in the areas close to the waste disposal sites their share was considerably lower. The differences between the studied urban soils were also found in the structure of soil yeast complexes. In urban soils with high anthropogenic impact, the isolation frequency of clinically important yeast species (Candida parapsilosis, C. tropicalis, Diutina catenulata, and Pichia kudriavzevii) was as high as 35% of all studied samples, while its share in the community was 17%. The factors responsible for development of specific features of yeast communities in various urban soils are discussed in the paper.     

Characterization of yeast groupings in the phyllosphere of <Emphasis Type="Italic">Sphagnum</Emphasis> mosses

Significant differences were revealed in the taxonomic structure of the epiphytic yeast communities formed on Sphagnum mosses and on the leaves of vascular plants. On mosses, low abundance of red yeasts was found (the most typical epiphytes on vascular plant leaves), along with a relatively high content and diversity of nonpigmented dimorphic basidiomycetes related to the order Leucosporidiales. The species composition of epiphytic yeasts from mosses is different from that of both forest and meadow grasses and of the parts of vascular plants submerged in the turf. The specific composition of the Sphagnum mosses yeast community is probably determined by the biochemical characteristics of this environment, rather than by the hydrothermal regime in the turf.     

MALDI-TOF MS Supplementary database for species identification employing the yeast diversity encountered on southern Brazil grapes

The study of grape microflora is of interest when autochthonous yeasts, which are related to typical wine characteristics, are intended to be used in winemaking. The election of matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) as the first method for yeast identification was based on its accuracy and rapidity compared to alternative laboratory protocols for identification. The aims of this study are to consolidate the MALDI-TOF MS Supplementary database for environmental yeasts already constructed, to expand it through the addition of standard spectra of not included yeast species, and to discuss the grape microflora encountered in Southern Brazil. A total of 358 strains, isolated from grape berries, were submitted to protein profiling employing Biotyper and Supplementary database. Molecular biology techniques were used as alternatives to identify 6.4% of strains not promptly designated by protein profiling. These strains corresponded to the species Candida californica, Zygoascus meyerae, Candida akabanensis, Candida azyma, and Hanseniaspora vineae. The MALDI-TOF MS spectra of the identified species were added to Supplementary database. The presented results strengthen the need for further expansion of the mass spectra database to broaden its microbiological application.     

From grape berries to wine: population dynamics of cultivable yeasts associated to “Nero di Troia” autochthonous grape cultivar

The aim of this work was to study the biodiversity of yeasts isolated from the autochthonous grape variety called “Uva di Troia”, monitoring the natural diversity from the grape berries to wine during a vintage. Grapes were collected in vineyards from two different geographical areas and spontaneous alcoholic fermentations (AFs) were performed. Different restriction profiles of ITS–5.8S rDNA region, corresponding to Saccharomyces cerevisiae, Issatchenkia orientalis, Metschnikowia pulcherrima, Hanseniaspora uvarum, Candida zemplinina, Issatchenkia terricola, Kluyveromyces thermotolerans, Torulaspora delbrueckii, Metschnikowia chrysoperlae, Pichia fermentans, Hanseniaspora opuntiae and Hanseniaspora guilliermondii, were observed. The yeast occurrences varied significantly from both grape berries and grape juices, depending on the sampling location. Furthermore, samples collected at the end of AF revealed the great predominance of Saccharomyces cerevisiae, with a high intraspecific biodiversity. This is the first report on the population dynamics of ‘cultivable’ microbiota diversity of “Uva di Troia” cultivar from the grape to the corresponding wine (“Nero di Troia”), and more general for Southern Italian oenological productions, allowing us to provide the basis for an improved management of wine yeasts (with both non-Saccharomyces and Saccharomyces) for the production of typical wines with desired unique traits. A certain geographical-dependent variability has been reported, suggesting the need of local based formulation for autochthonous starter cultures, especially in the proportion of the different species/strains in the design of mixed microbial preparations.     

Characterization of the fungal flora of dolo,a traditional fermented beverage of Burkina Faso,using MALDI-TOF mass spectrometry

A cross-sectional study was conducted in Bobo-Dioulasso, Burkina Faso, to identify the yeast diversity associated with the manufacture of dolo, a traditional fermented beverage of Burkina Faso. From sixty specimens spread onto chromogenic medium plates, sixty-two strains were isolated then identified using MALDI-TOF analysis. Seven yeast species were identified, Saccharomyces cerevisiae (39%) followed by Pichia manshurica (18%) being the most frequent. Forty-three percent of the samples contained Candida species, notably Candida albicans. In conclusion, the combined use of a chromogenic medium and MALDI-TOF analysis reveals a higher diversity in yeast species present in the dolo than previously thought.     

Identification of yeasts during alcoholic fermentation of <Emphasis Type="Italic">tchapalo</Emphasis>, a traditional sorghum beer from Côte d’Ivoire

This study investigated the diversity and dynamics of yeasts involved in alcoholic fermentation of a traditional sorghum beer from Côte d’Ivoire, tchapalo. A total of 240 yeast strains were isolated from fermenting sorghum wort inoculated with dry yeast from two geographic regions of Côte d’Ivoire (Abidjan and Bondoukou). Initial molecular identification to the species level was carried out using RFLP of PCR-amplified internal transcribed spacers of rDNA (ITS1-5.8S-ITS2). Ten different profiles were obtained from the restriction of PCR products with the three endonucleases HaeIII, CfoI and HinfI. Sequence analysis of the D1/D2 domain of the 26S rDNA and the ACT1 gene allowed us to assign these groups to six different species: Saccharomyces cerevisiae-like, Candida tropicalis, Pichia kudriavzevii, Pichia kluyveri, Kodamaea ohmeri and Meyerozyma caribbica. The most frequent species associated with tchapalo fermentation was S. cerevisiae-like (87.36%), followed by C. tropicalis (5.45%) and M. caribbica (2.71%). S. cerevisiae-like strains were diploid heterozygotes and exhibited three to four nucleotides divergence from the type strain in the D1/D2 domain and several indels in the more discriminant sequence of the intron of the ACT1 gene. During the process, the yeast species isolated and their frequencies varied according to the geographic origin of the dry yeast. The occurrence of some species was sporadic and only two non-Saccharomyces species were found in the final product.     

Usefulness of the Non-conventional <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> Model to Assess <Emphasis Type="Italic">Candida</Emphasis> Virulence

Invasive candidiasis is caused mainly by Candida albicans, but other Candida species have increasing etiologies. These species show different virulence and susceptibility levels to antifungal drugs. The aims of this study were to evaluate the usefulness of the non-conventional model Caenorhabditis elegans to assess the in vivo virulence of seven different Candida species and to compare the virulence in vivo with the in vitro production of proteinases and phospholipases, hemolytic activity and biofilm development capacity. One culture collection strain of each of seven Candida species (C. albicans, Candida dubliniensis, Candida glabrata, Candida krusei, Candida metapsilosis, Candida orthopsilosis and Candida parapsilosis) was studied. A double mutant C. elegans AU37 strain (glp-4;sek-1) was infected with Candida by ingestion, and the analysis of nematode survival was performed in liquid medium every 24 h until 120 h. Candida establishes a persistent lethal infection in the C. elegans intestinal tract. C. albicans and C. krusei were the most pathogenic species, whereas C. dubliniensis infection showed the lowest mortality. C. albicans was the only species with phospholipase activity, was the greatest producer of aspartyl proteinase and had a higher hemolytic activity. C. albicans and C. krusei caused higher mortality than the rest of the Candida species studied in the C. elegans model of candidiasis.     

Assessment of endophytic yeast diversity in rice leaves by a culture-independent approach

Endophytic microorganisms inhabit internal plant tissues in the host plant without causing any symptoms or negative effects. Although the diversity of endophytes has been evaluated by both culture-dependent and culture-independent methods, less information is available on yeast communities. Therefore, in this study a culture-independent method was used to examine endophytic yeasts associated with rice leaves based on the large subunit of ribosomal DNA using a semi-nested PCR technique. Sequence analysis indicated that the colonization frequency and the relative species frequency (RF) of endophytic yeast phylotypes were 0.41 and 0.06, respectively, and the majority of the yeast phylotypes were basidiomycetous yeasts. The phylotypes were designated as five known species (Cryptococcus victoriae, Debaryomyces hansenii, Debaryomyces vindobonensis, Meyerozyma guilliermondii and Pseudozyma antarctica), together with seventeen phylotypes closest to Candida metapsilosis, Cryp. foliicola, Cryp. laurentii, Pseudozyma abaconensis, Pseudozyma aphidis and Trichosporon asahii, among which some could be novel species. The most prevalent phylotypes were those closest to Cryp. foliicola (47.5 % RF) followed by D. hansenii (22.8 % RF) and P. antarctica (16.8 % RF). The presence of the phylotypes related to species known for their potential applications as biocontrol agents and plant growth promoting hormone producers suggests that they may have valuable applications. In addition, our findings revealed the occurrence of novel phylotypes at high frequency, which should encourage extensive studies to discover novel yeast species and to understand their roles in the rice leaves.     

Molecular genetic polymorphism of soil yeasts of the genus <Emphasis Type="Italic">Williopsis</Emphasis> from Taiwan Island

Comparative molecular genetic study of Williopsis yeasts isolated in different world regions reveals some peculiarities of species content in Taiwan. Some Williopsis yeasts may represent novel species. In Taiwan, four of the five known Williopsis species are documented: W. saturnus, W. suaveolens, W. mrakii, and W. subsufficiens. The W. saturnus yeasts predominate in Taiwanese soils, while W. suaveolens is more frequently isolated in Europe.     

Massive isolation of anamorphous ascomycete yeasts <Emphasis Type="Italic">Candida oleophila</Emphasis> from plant phyllosphere

Many years of research has confirmed a wide distribution of anamorphous ascomycete yeasts in the phyllosphere of diverse plants of Moscow and the Moscow oblast. Based on the standard morphological and physiological criteria, on the results of restriction analysis of the 5.8S-ITS rDNA region, and on the sequencing of the D1D2 region of 26S rDNA, these yeasts were identified as Candida oleophila Montrocher. Previous isolation of this species has been rare, possibly due to its incorrect identification. This species, together with phytobiotic basidiomycete yeasts, was shown to be dominant in the yeast epiphytic communities on the surface parts of plants. The relative abundance of C. oleophila is highest on plant fruits and increases significantly by the end of the vegetation period. Wide occurrence of this yeast species on fruits and in the phyllosphere may be related to its ability to compete with rapidly growing phytopathogenic fungi.     

Yeast communities of <Emphasis Type="Italic">Formica aquilonia</Emphasis> colonies

Yeast abundance and species diversity in the colonies of Formica aquilonia ants in birch–pine grass forest near Novosibirsk, Russia, were studied. The average yeast number in the anthill material was 10³–10⁴ CFU/g, reaching 10⁵ CFU/g in the hatching chambers. Typical litter species (Trichosporon moniliiforme and Cystofilobasidium capitatum) were predominant in soil and litter around the anthills. Apart from these species, ascomycete species of the family Debaryomycetaceae, Debaryomyces hansenii, and Schwanniomyces vanrijiae were predominant in the anthill material. Yeast population of the ant’ bodies consisted exclusively of the members of the last two species. Thus, highly specific yeast communities formed in the colonies of Formica aquilonia ants differ from the communities of surrounding soil. These differences are caused by environment-forming activity of the ants.     

The diversity of culturable yeasts in the phylloplane of rice in Thailand

One hundred and fifty-six yeast strains were obtained by the enrichment technique from the phylloplanes of 85 rice leaf samples collected from seven provinces in Thailand. On the basis of the D1/D2 domain of the large subunit rRNA gene sequence analysis, 156 strains were identified as 34 known species in 18 genera consisting of 25 species in 13 genera of the phylum Ascomycota and nine species in five genera of the phylum Basidiomycota. The species in the phylum Ascomycota comprised 24 species in 12 genera of the order Saccharomycetales and one species viz. Yarrowia lipolytica in Saccharomycetales incertae sedis. The 24 species viz. Candida glabrata in the Nakaseomyces clade of Saccharomycetaceae, Candida jaroonii, Candida membranifaciens and Candida terebra in the Yamadazyma clade of Debaryomycetaceae, Candida pseudolambica in the Pichia clade of Pichiaceae, Candida ruelliae in the Metschnikowia clade of Metschnikowiaceae, and three unaffiliated clade Candida species (Candida catenulata, Candida rugosa and Candida tropicalis); Clavispora lusitaniae, Kodamaea ohmeri, Metschnikowia koreensis and Metschnikowia lopburiensis in Metschnikowiaceae; Cyberlindnera fabianii, Cyberlindnera rhodanensis and Wickerhamomyces ciferrii in Wickerhamomycetaceae; Debaryomyces nepalensis, Meyerozyma caribbica, Meyerozyma guilliermondii, Millerozyma koratensis, and Yamadazyma mexicanum in Debaryomycetaceae; Pichia kudriavzevii in Pichiaceae; and Lachancea thermotolerans in Saccharomycetaceae. The species in Basidiomycota viz. Cryptococcus flavescens, Cryptococcus laurentii, Cryptococcus aff. laurentii and Cryptococcus rajasthanensis in the Tremellales lineage, Bulleromyces clade, Tremellales, Tremellomycetes, Agaricomycotina; Pseudozyma antarctica and Pseudozyma aphidis in Ustilaginales, Ustilaginomycetes, Ustilaginomycotina; Rhodotorula taiwanensis and Sporobolomyces blumeae in Sporidiobolales, Microbotryomycetes, Pucciniomycotina; and Trichosporon asahii in Trichosporonales, Tremellomycetes, Agaricomycotina. The most prevalent species was R. taiwanensis with a 23 % frequency of occurrence followed by Candida tropicalis (16 %) and Cryptococcus fabianii (12 %).     

Methods of <Emphasis Type="BoldItalic">Candida dubliniensis</Emphasis> identification and its occurrence in human clinical material

Candida dubliniensis was reported as a new species in 1995. This species is often misidentified as Candida albicans. The aims of this work were to determine the occurrence of C. dubliniensis in various clinical materials, to evaluate several ways to identify it and to examine the genetic variability of isolates. Among 7706 isolates originally identified as C. albicans, 237 were identified as C. dubliniensis (3.1%). Most of the C. dubliniensis isolates were obtained from the upper and lower respiratory tract (61.4 and 22.9%). Five phenotypic methods including latex agglutination were used (cultivation on CHROMagar Candida, on Staib agar, at 42 °C and in medium with 6.5% NaCl), but only cultivation on the medium with an increased concentration of NaCl and latex agglutination gave reliable results. Species-specific polymerase chain reaction was used as the confirmation method. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry provided less reliable results. In fact, 78.9% of C. dubliniensis isolates had scores above 1.7. However, the rest of them (21.1%) were also identified as C. dubliniensis even when the scores were lower than 1.7. Divergences among C. dubliniensis strains were evaluated by means of pulsed-field gel electrophoresis. Eighty-six selected C. dubliniensis isolates showed a 69.6% level of similarity. The results of this study expand the knowledge of the incidence, means of identification and genotypic divergence of C. dubliniensis isolates.     

Endophytic yeasts in leaf galls

Yeast abundance and species diversity of endophytic complexes in galls (cecidia) formed on the leaves of Salix fragilis, Salix caprea, Quercus robur, Tilia cordata, and Ulmus laevis and the epiphytic yeast communities of undamaged leaves of these plants were studied. Dynamics of yeast abundance in the galls was significantly different from that of the epiphytic yeast communities. Maximum numbers of endophytic yeast cells in the galls (up to 10⁴ CFU/g) were comparable to abundance of epiphytic yeasts. A total of 14 species of endophytic yeasts were isolated from galls of different plants. Ascomycetous yeasts were found to predominate in the insect galls on willows and oak, while basidiomycetous yeasts dominated in mite galls on linden and elm, as well as on plant leaves. These results indicate that gall formation may be considered not only as a bidirectional pathological process of the interaction between plants and invertebrates, but also as a process in which the endophytic microbial population of the galls plays an important role.     

Genetic relationship and biological status of the industrially important yeast <Emphasis Type="Italic">Saccharomyces eubayanus</Emphasis> Sampaio et al.

The genomes of the recently discovered yeast Saccharomyces eubayanus and traditional S. cerevisiae are known to be found in the yeast S. pastorianus (syn. S. carlsbergensis), which are essential for brewing. The cryotolerant yeast S. bayanus var. uvarum is of great importance for production of some wines. Based on ascospore viability and meiotic recombination of the control parental markers in hybrids, we have shown that there is no complete interspecies post-zygotic isolation between the yeasts S. eubayanus, S. bayanus var. bayanus and S. bayanus var. uvarum. The genetic data presented indicate that all of the three taxa belong to the same species.