Application of different molecular techniques for deciphering genetic diversity among yeast isolates of traditional fermented food products of Western Himalayas

Molecular and Technological Characterization of Saccharomyces cerevisiae from Sourdough

DNA markers help detect the intraspecific genetic diversity of yeast strains. Eight ISSR (Inter Simple Sequence Repeats) primers were used to assess the intraspecific diversity of Saccharomyces cerevisiae (n = 96) from different populations (n = 3), evaluate the technological characteristics, and investigate trait-loci associations. The primers amplified 154 reproducible and scorable bands, of which 79.87% were polymorphic. The UPGMA (unweighted pair group method with arithmetic mean) dendrogram clustered 96 isolates into two main clusters, supported by STRUCTURE HARVESTER results (ΔK = 2). Analysis of molecular variance (AMOVA) indicated significant genetic differences between (15%) and within the populations (85%) (p < 0.001). Twenty-nine genetically distinct strains were selected for the technological characterization. Principal component analysis (PCA) revealed that five strains with high fermentation capacity, leavening activity, high growth index at 37 °C, and harsh growth conditions were technologically relevant. Trait-loci association analyses indicated that the highest correlation (r = 0.60) was recorded for the fermentation capacity on the 8th and 113th loci, amplified by ISSR-1 and ISSR-6 primers, respectively (p < 0.05). The strains yielding high performances and the associated loci amplified by ISSR markers possess a high potential to generate locus-specific primers to target the strains with high fermentation capacity.

Insights into the ecology of Schizosaccharomyces species in natural and artificial habitats

The fission yeast genus Schizosaccharomyces contains important model organisms for biological research. In particular, S. pombe is a widely used model eukaryote. So far little is known about the natural and artificial habitats of species in this genus. Finding out where S. pombe and other fission yeast species occur and how they live in their habitats can promote better understanding of their biology. Here we investigate in which substrates S. pombe, S. octosporus, S. osmophilus and S. japonicus are present. To this end about 2100 samples consisting of soil, tree sap fluxes, fresh fruit, dried fruit, honey, cacao beans, molasses and other substrates were analyzed. Effective isolation methods that allow efficient isolation of the above mentioned species were developed. Based on the frequency of isolating different fission yeast species in various substrates and on extensive literature survey, conclusions are drawn on their ecology. The results suggest that the primary habitat of S. pombe and S. octosporus is honeybee honey. Both species were also frequently detected on certain dried fruit like raisins, mango or pineapple to which they could be brought by the honey bees during ripening or during drying. While S. pombe was regularly isolated from grape mash and from fermented raw cacao beans S. octosporus was never isolated from fresh fruit. The main habitat of S. osmophilus seems to be solitary bee beebread. It was rarely isolated from raisins. S. japonicus was mainly found in forest substrates although it occurs on fruit and in fruit fermentations, too.

Evaluation of genetic diversity and development of core collections of industrial brewing yeast using ISSR markers

Germplasm of industrial brewing yeast of the worldwide have a richer diversity, and various successes in improving the performance of brewing yeasts. However, they are limited in that they have relatively low odds of combining desirable traits in a correct manner. To improve germplasm resource preservation, management, and utilization efficiency. In this study, the genetic diversity of 35 industrial brewing yeasts were analyzed based upon inter simple sequence repeat (ISSR) markers, in which 151 out of 167 SSR loci (90.42%) were polymorphic between two or more strains. Three preliminary core collections were established using ISSR data, and based on three different strategies as follows: an advanced maximization (M) strategy, an allele preferred sampling (A) strategy, and a random sampling (R) strategy. Comparison of genetic parameters, including polymorphic information content, Nei's genetic diversity (H), effective allele number, observed allele number, Shannon's index (I), and principal coordinate analyses, confirmed that all the core collections accurately recapitulated the diversity of the initial germplasm. Considering the loci retention ratio and trait coverage efficiency, Core1 was considered the best core collection.

The utility of iPBS retrotransposons markers to analyze genetic variation in yeast

Yeasts are one of the main organisms in the food industry and effective components of many ecosystems. The method for identifying and detecting certain yeast species or strains is a crucial step for the food industry and should be simple, reliable, fast, and inexpensive. In our study, inter-priming binding sites (iPBS) retrotransposon marker system was employed to elucidate the genetic variability at intraspecies and interspecies levels among 112 yeast strains belonging to eight species previously obtained from fermented foods. The molecular identification of yeast strains was firstly confirmed by sequencing the D1/D2 domain of the 26S rRNA. The eight selected retrotransposon-based primers produced 278 bands, all of which were polymorphic with an average of 34.75 polymorphic fragments per primer. The averages of polymorphism information contents and the resolving power values for the iPBS marker system were 0.23 and 10.11, respectively. The genetic parameters within each yeast species obtained from iPBS markers were observed as; the percentage of polymorphic loci for each species ranging from 19.23% to 71.21%, Nei's gene diversity from 0.085 to 0.228, while Shannon's information index values ranging from 0.125 to 0.349. The value of gene flow (0.09) and genetic variation among the populations (0.85) showed higher genetic variation among the species. UPGMA analyses demonstrated considerable genetic variability in the yeast strains, clustered them according to their species, and revealed the intraspecific variation. Each of the selected iPBS primer provided enough species-discrimination. Present evaluations suggest the utility of iPBS marker system to estimate the genetic variation of yeast strains. This study is a preliminary point for further studies on the identification methodology, and population genetics of yeast species having importance in the food industry with iPBS markers.

Schizosaccharomyces pombe Biotechnological Applications in Winemaking

The traditional way of producing wine is through the use of Saccharomyces cerevisiae in order to convert glucose and fructose into alcohol. In the case of red wines, after this alcoholic fermentation lactic bacteria Oenococus oeni is used to stabilize wine from a microbiological point of view by converting malic acid into lactic acid that it is not a microbiological substract. The yeast species Schizosaccharomyces pombe was traditionally considered spoilage yeast. Nevertheless, during the last decade it started to be used due to its unique malic acid deacidification ability to reduce the harsh acidity of wines from northern Europe, by converting malic acid to ethanol and CO₂ without producing lactic acid as lactic bacteria does. Additionally, during the last years, S. pombe has started to be used to solve the problems of modern winemaking industry such as increasing food quality or food safety. Some of those new uses, different from its traditional malic acid deacidification, are: high autolytic polysaccharides release, gluconic acid reduction, urease activity that make impossible ethyl carbamate (toxic compound) formation, high pyruvic acid production, that is related to color improvement, and removing lactic bacteria subtracts while avoiding biogenic amines (toxic compounds such as histamine) formation.

Schizosaccharomyces pombe Isolation Protocol

This chapter describes a methodology to isolate yeast strains from Schizosaccharomyces pombe species. The method is based on a selective-differential medium that notably facilitates the isolation of S. pombe. The main difficulty in isolating microorganisms from this genus is their extremely low incidence in nature when they are compared to other microorganisms. The proposed methodology allows isolating and selecting strains from this species for industrial purposes. Methodologies allows detecting the presence of those yeasts when they are considered spoilage microorganisms. Several selective-differential agents based on the basic physiological characteristics of S. pombe species are exposed during the chapter introduction and the use is properly justified. Some of those representative characteristics are its extraordinary resistance to high sugar concentrations, sulfur dioxide, sorbic acid, benzoic acid, acetic acid, or their unique malo-ethanolic fermentation ability. The proposed selective medium is mainly based on S. pombe resistance to the antibiotic actidione and the unusual tolerance to the inhibitory agent benzoic acid compared to possible microorganisms that could produce false-positive results during an isolation process. In addition, malic acid is proposed as the main differential factor due to the exclusive ability of this species to metabolize malic acid into ethanol. This fact allows the detection of malic acid degradation. Cloramphenicol is used to inhibit bacteria growth and liquid media to avoid fungi development.

Fermentation of Apple Juice with a Selected Yeast Strain Isolated from the Fermented Foods of Himalayan Regions and Its Organoleptic Properties

Twenty-three Saccharomyces cerevisiae strains isolated from different fermented foods of Western Himalayas have been studied for strain level and functional diversity in our department. Among these 23 strains, 10 S. cerevisiae strains on the basis of variation in their brewing traits were selected to study their organoleptic effect at gene level by targeting ATF1 gene, which is responsible for ester synthesis during fermentation. Significant variation was observed in ATF1 gene sequences, suggesting differences in aroma and flavor of their brewing products. Apple is a predominant fruit in Himachal Pradesh and apple cider is one of the most popular drinks all around the world hence, it was chosen for sensory evaluation of six selected yeast strains. Organoleptic studies and sensory analysis suggested Sc21 and Sc01 as best indigenous strains for soft and hard cider, respectively, indicating their potential in enriching the local products with enhanced quality.

Fructanase and fructosyltransferase activity of non-Saccharomyces yeasts isolated from fermenting musts of Mezcal

Fructanase and fructosyltransferase are interesting for the tequila process and prebiotics production (functional food industry). In this study, one hundred thirty non-Saccharomyces yeasts isolated from "Mezcal de Oaxaca" were screened for fructanase and fructosyltransferase activity. On solid medium, fifty isolates grew on Agave tequilana fructans (ATF), inulin or levan. In liquid media, inulin and ATF induced fructanase activities of between 0.02 and 0.27U/ml depending of yeast isolate. High fructanase activity on sucrose was observed for Kluyveromyces marxianus and Torulaspora delbrueckii, while the highest fructanase activity on inulin and ATF was observed for Issatchenkia orientalis, Cryptococcus albidus, and Candida apicola. Zygosaccharomyces bisporus and Candida boidinii had a high hydrolytic activity on levan. Sixteen yeasts belonging to K. marxianus, T. delbrueckii and C. apicola species were positive for fructosyltransferase activity. Mezcal microbiota proved to showed to be a source for new fructanase and fructosyltransferases with potential application in the tequila and food industry.