D. Gouliamova

Two yeast species Cystobasidium psychroaquaticum f.a. sp. nov. and Cystobasidium rietchieii f.a. sp. nov. isolated from natural environments, and the transfer of Rhodotorula minuta clade members to the genus Cystobasidium.

AbstractnMany species of dimorphic basidiomycetes are known only in their asexual phase and typically those pigmented in different hues of red have been classified in the large polyphyletic genus Rhodotorula. These yeasts are ubiquitous and include a few species of some clinical relevance. The phylogenetic distribution of Rhodotorula spans three classes: Microbotryomycetes, Cystobasidiomycetes and Exobasidiomycetes. Here, the presented multi-gene analyses resolved phylogenetic relationships between the second largest group of Rhodotorula and the mycoparasite Cystobasidium fimetarium (Cystobasidiales, Cystobasidiomycetes, Pucciniomycotina). Based on the results, we propose the transfer of nine species belonging to the Rhodotorula minuta clade into the genus Cystobasidium. As a result, the clinically relevant species R. minuta will be renamed Cystobasidium minutum. This proposal follows ongoing reassessments of the anamorphic genus Rhodotorula reducing the polyphyly of this genus. The delimitation of the R. minuta clade from Rhodotorula species comprised in Sporidiobolales including the type species Rhodotorula glutinis is an important step to overcome obsolete generic placements of asexual basidiomycetous yeasts. Our proposal will also help to distinguish most common red yeasts from clinical samples such as members of Sporidiobolales and Cystobasidiales. The diagnosis of the genus Cystobasidium is amended by including additional characteristics known for the related group of species. The taxonomic change enables us to classify two novel species with the phylogenetically related members of the R. minuta clade in Cystobasidium. The recently from natural environments isolated species are described here as Cystobasidium psychroaquaticum f.a. sp. nov. (K-833Txa0=xa0KBP 3881Txa0=xa0VKPM Y-3653Txa0=xa0CBSxa011769Txa0=xa0MUCL 52875Txa0=xa0DSM 27713T) and Cystobasidium rietchiei f.a. sp. nov. (K-780Txa0=xa0KBP 4220Txa0=xa0VKPM Y-3658Txa0=xa0CBSxa012324Txa0=xa0MUCL 53589Txa0=xa0DSM 27155T). The new species were registered in MycoBank under MB 809336 and MB 809337, respectively.

Ecophysiological properties of cultivable heterotrophic bacteria and yeasts dominating in phytocenoses of Galindez Island, maritime Antarctica

Antarctic plants are stable specific microenvironments for microbial colonization that are still less explored. In this study, we investigated cultivable heterotrophic bacteria and yeasts dominating in plant samples collected from different terrestrial biotopes near Ukrainian Antarctic Base on Galindez Island, maritime Antarctica. Phylogenetic analysis revealed affiliation of the bacterial isolates to genera Pseudomonas, Stenotrophomonas, Brevundimonas, Sporosarcina, Dermacoccus, Microbacterium, Rothia and Frondihabitans, and the yeast isolates to genera Rhodosporidium, Cryptococcus, Leucosporidiella, Candida and Exophiala. Some ecophysiological properties of isolated strains were determined that are important in response to different stresses such as psychro- and halotolerance, UV-resistance and production of hydrolytic enzymes. The majority of isolates (88xa0%) was found to be psychrotolerant; all are halotolerant. Significant differences in survival subsequent to UV-C radiation were observed among the isolates, as measured by culturable counts. For the bacterial isolates, lethal doses in the range 80–600xa0Jxa0m−2 were determined, and for the yeast isolates—in the range 300–1,000xa0Jxa0m−2. Dermacoccus profundi U9 and Candida davisiana U6 were found as most UV resistant among the bacterial and yeast isolates, respectively. Producers of caseinase, gelatinase, β-glucosidase, and cellulase were detected. To the best of our knowledge, this is the first report on isolation of UV resistant strain D. profundi, and Frondihabitans strain from Antarctica, and on detection of cellulase activity in Antarctic yeast strain C. davisiana. The results obtained contribute to clarifying adaptation strategies of Antarctic microbiota and its possible role in functional stability of Antarctic biocenoses. Stress tolerant strains were detected that are valuable for ecological and applied studies.

Ogataea saltuana sp. nov., a novel methanol-assimilating yeast species

Four ascosporulating strains of an undescribed methanol-assimilating yeast species were isolated from forest habitats in Hungary. Three were recovered from rotten wood and one from leaves of a sessile oak (Quercus petraea). An additional isolate of the undescribed species sharing similar phenotypic characters with the above-noted strains was recovered from the gut of an unidentified beetle collected from under the bark of a coniferous tree in Bulgaria. A closely related, but somewhat divergent strain was recovered from insect frass in a Ponderosa pine (Pinus ponderosa) collected in New Mexico, USA. Analysis of the D1/D2 sequences of the LSU rRNA gene placed the new species in the Ogataea clade. The ITS and the D1/D2 LSU sequences of the rRNA gene repeats were compared for the above-noted strains and that of the type strain of Ogataea zsoltii, the closest neighbour among currently recognized Ogataea species. Their relatedness was investigated by parsimony network analysis as well. As a result of the sequence analysis, it was concluded that the six strains isolated from tree associated habitats represent a single new yeast species. Ogataea saltuana sp. nov. is proposed to accommodate these strains. The type strain NCAIM Y.01833T (CBS 10795T, NRRL Y-48448T) was recovered from rotten wood of Scotch pine (Pinus silvestris) in Hungary. The GenBank accession number for the D1/D2 domain nuclear large subunit rRNA gene sequence of strain NCAIM Y.01833T (CBS 10795T, NRRL Y-48448T) is EU327033. The MycoBank number of the new species is MB 519966.

Rapid screening of plasmid-encoded small hsp-genes in Streptococcus thermophilus

A new rapid procedure for detection of small heat shock protein genes (shsp) was developed. Using PCR-based molecular approach, single colonies of 49 Streptococcus thermophilus industrial and artisanal starters were examined. Five strains contained plasmid-encoded shsp. The nucleotide sequence analysis revealed that the genes are very conservative, as only a few nucleotide substitutions were noticed. It was shown that all new isolated plasmids belong to the pC194 family of rolling circle replicating (RCR) plasmids. We concluded that shsp genes are always inherited together with pC194-type replicative region. The viability of plasmid-bearing and plasmid-free derivatives of S. thermophilus strain ST2980 under heat shock condition was studied.

DNA barcoding revealed Nematodospora valgi gen. nov., sp. nov. and Candida cetoniae sp. nov. in the Lodderomyces clade

During a yeast biodiversity survey conducted in 2009-2011 in Bulgaria (South Eastern Europe) five strains of a novel ascomycetous yeast species were isolated from the beetle Valgus hemipterus (Cetoniinae) collected from two localities, namely Osogovska Planina Mountain and Nature Park Zlatni Pyasatsi. Phylogenetic analysis using combined sequences of the D1/D2 domains of the large subunit ribosomal DNA (LSU rDNA) and the internal transcribed spacers 1 + 2 regions (ITS1+2) placed the novel species on a separate branch near the basal part of the Lodderomyces clade. The novel species has a unique ascospore morphology distinct from those of the closely related teleomorphic genus Lodderomyces. Based on phylogenetic analysis and morphology of the ascospores we propose Nematodospora valgi gen. nov., sp. nov. to accommodate these isolates (MB811804 D37S(T), MB802458). Two strains of a novel anamorphic yeast species were isolated from the beetles Cetonia aurata and Oxythyrea funesta (Cetoniinae) collected in East Rhodopies and Sofia city, respectively. DNA barcoding analysis placed the new yeast species within the Candida parapsilosis subclade. Here, we present the description of a new yeast species, Candida cetoniae sp. nov. (IMB1R2(T), MB803501) to accommodate these two strains. The ecology and biogeography of the insect-associated yeasts of the Lodderomyces clade is discussed.

DNA Barcoding of Yeasts from Selected Bulgarian Food Products

ABSTRACT Studies on biodiversity of yeasts in Bulgarian food ecosystems are scarce. In present article 14 yeast strains were isolated from various commercial Bulgarian food products and characterized by DNA barcoding analysis. The analysis has shown occurrence in food products various yeasts from the following genera- Saccharomyces, Kazachstania, Kluyveromyces, Pichia, Isatchenkia, Candida and Rhodotorula.

Preliminary Characterization of Yeasts and Actinomycetes Isolated from Mammalian Feces

ABSTRACT Yeasts and actinomycetes isolated from fecal pellets of various mammals from a zoo in Sofia, Bulgaria were identified using DNA barcoding analysis. The analysis has shown that yeast strains belong to the ascomycete genera Kluyveromyces, Clavispora, Pichia, Wickerhamomyces, Candida, Zygowilliopsis, Galactomyces, Hanseniaspora, and Debaryomyces. Basidiomycete yeasts belong to the genera Trichosporon, Cryptococcus, Rhodotorula and Guehomyces. All actinomycete strains were identified as Thermoactinomyces saccharii. Additionally, extracellular enzymatic activity and ability to grow at various temperatures of isolated strains were analyzed.

New Method for Sequence Alignment Based on Probabilities of Nucleotide Correspondences

ABSTRACT The objective of our work is to develop a general method for structurally related, but diverged sequences for simultaneous optimization of alignment and self-folding—the so-called Sankoffs program for simultaneous prediction of secondary structure and alignment between nucleotide sequences. A simple reason behind the simultaneous optimization of alignment and self-folding is that strong structural consensus among related, but diverged sequences are a good indicator for preserved functional role. Up to now there is no a general solution for this long standing problem. Here we discuss an approach which is just a first step to the full realization of Sankoffs program. Currently available models and software packages, such as foldalign, dynalign and others, implement only restricted versions (variations around first align and then fold or oppositely) of Sunkoffs program and do not use the full loop-based RNA/DNA energy model. We divided Sankofs program in two steps based on the analogy between the classical alignment algorithm and hybridization without self-folding. The next step is to include in the alignment an algorithm for the self-folding. In our approach, the alignment problem requires the implementation of the full loop-based RNA/DNA energy model for hybridization of two sequences. For this, we divided the alignment between two sequences into loops and associated a score to each loop in such way that the total score of the alignment is a sum over the scores for each alignment loop. The loop scoring model for alignment consists of following loop types: stacking with matched and mismatched pairs, bulges, internal loops and dangling ends. Calculation of thermodynamic partition function over all possible double-stranded conformations is interpreted in terms of all possible canonical pairwise alignments. The partition function is computed by means of a dynamic programming algorithm and used to determine the probability of an alignment as well as the probability of each possible match between two sequence positions. For calculation of match probabilities detailed recursion relations for partition functions of alignments are based on their recursion analogs for hybridization of subsequences. The partition function is used for backtracking and reconstructing a properly weighted ensemble of optimal and suboptimal alignments.

Molecular Study of the useful and the Contaminant Microflora in Fermented Dairy Products

ABSTRACT Lactic acid bacteria have been used as starter strains in the production of fermented dairy products for centuries. Most of the dairy products contain lactic acid bacteria, but also other bacteria involved as contaminant microflora. We explored the microbial content of home-made dairy products and those purchased from the market. In our study twenty-six pure cultures were isolated. The isolated strains were investigated by a set of physiological and molecular-genetic methods for their accurate species identification and genotyping. From the microorganisms, involved in fermentation and ripening of dairy products with proven health benefits to human, in studied foods predominated Lactobacillus delbrueckii, Lactobacillus helveticus and Lactobacillus plantarum. Another part of the isolated strains, representatives of the genus Kluyveromyces, Rhodotorula and Candida were contaminant microflora, as a result of poor hygiene in the manufacture and storage of the dairy products. Some of these strains were isolated from commercially available dairy products. The obtained results raise again the question about the efficacy of microbiological quality control and food safety.

Biological Sequence Comparison, Molecular Evolution and Phylogenetics

ABSTRACT For closely related sequences there is a single optimal alignment which provides an accurate measure of similarity, structure, function and evolutionary history. However, with increasing evolutionary distances between nucleotide sequences the single optimal alignment method is replaced by an ensemble of alignments of almost equal quality and ensemble of different self-folded conformations. Recurring difficulties associated with diverged sequence data include alternative alignment possibilities of insertions and deletions, region of length variations in which homology assessment is questionable or impossible, occurrence of localized excessive mutations to the point of saturation and lost of phylogenetic signals. Therefore, for diverged sequences optimizing similarity will not necessarily improve structure, function and evolutionary history assessments. Here our aim is to present an overview of the methods involved in sequence analysis which are critical for current theoretical and application development. However, we do not follow historical events. For sequence comparison we focus on those methods that are based on exhaustive schemes, which are classically formulated as dynamic programming algorithms. They consist either of optimization schemes which find the best alignment for a given model, or of probabilistic schemes based on partition functions—in which all alignments, with their respective weights, are evaluated.